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Publications (10 of 39) Show all publications
Elmhalli, F., Garboui, S. S., Karlson, A. K. B., Mozuraitis, R., Baldauf, S. L. & Grandi, G. (2019). The repellency and toxicity effects of Essential oils from the Libyan plants Salvadora persica and Rosmarinus officinalis against nymphs of Ixodes ricinus.. Experimental & applied acarology, 77(4), 585-599
Open this publication in new window or tab >>The repellency and toxicity effects of Essential oils from the Libyan plants Salvadora persica and Rosmarinus officinalis against nymphs of Ixodes ricinus.
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2019 (English)In: Experimental & applied acarology, ISSN 0168-8162, E-ISSN 1572-9702, Vol. 77, no 4, p. 585-599Article in journal (Refereed) Published
Abstract [en]

Essential oils extracted from the leaves of Libyan Rosemary (Rosmarinus officinalis L.), and Miswak (Salvadora persica L.) were evaluated for their acaricidal and repellent effects on Ixodes ricinus L. nymphs (Acari: Ixodidae) using a bioassay based on an “open filter paper method".  R. officinalis leaf essential oil diluted to 0.5 and 1µl/cm ² in acetone exhibited, respectively, 20% and 100% tick mortality after about 5 hours of exposure. A total of 50% and 95% of I. ricinus nymphs were killed by direct contact with the oil when exposed to lethal concentrations (LC) of 0.7µl/cm² (LC50) and 0.95 µl/cm² (LC95), respectively. The LC50 (0.5µl/cm²) was reached before the end of the first 24 hours of exposure time (ET), as tick mortality at 24 hours was 60%. S. persica leaf essential oil at 1µl/cm² showed a significant repellency effect against I. ricinus nymphs at 1.5 hours ET. A 95% repellency was observed at a repellent concentration (RC95) of 1µl/cm² of S. persica, but no significant mortality was recorded at this dose of S. persica oil. Gas chromatography-mass spectrometry analyses showed that the main monoterpenes in both oils were 1,8-cineol, α-pinene, and β-pinene, although in markedly different proportions. These results suggest that essential oils have substantial potential as alternative approaches for I. ricinus tick control.

Keywords
Rosmarinus officinalis, Salvadora persica, essential oils, acaricidal, Ixodes ricinus.
National Category
Zoology
Research subject
Biology with specialization in Systematics
Identifiers
urn:nbn:se:uu:diva-381130 (URN)10.1007/s10493-019-00373-5 (DOI)000468592300010 ()31089978 (PubMedID)
Available from: 2019-04-04 Created: 2019-04-04 Last updated: 2019-08-28Bibliographically approved
Baldauf, S. L., Romeralo, M., Fiz-Palacios, O. & Heidari, N. (2018). A Deep Hidden Diversity of Dictyostelia. Protist, 169(1), 64-78
Open this publication in new window or tab >>A Deep Hidden Diversity of Dictyostelia
2018 (English)In: Protist, ISSN 1434-4610, E-ISSN 1618-0941, Vol. 169, no 1, p. 64-78Article in journal (Refereed) Published
Abstract [en]

Dictyostelia is a monophyletic group of transiently multicellular (sorocarpic) amoebae, whose study is currently limited to laboratory culture. This tends to favour faster growing species with robust sorocarps, while species with smaller more delicate sorocarps constitute most of the group’s taxonomic breadth. The number of known species is also small (∼150) given Dictyostelia’s molecular depth and apparent antiquity (>600 myr). Nonetheless, dictyostelid sequences are rarely recovered in culture independent sampling (ciPCR) surveys. We developed ciPCR primers to specifically target dictyostelid small subunit (SSU or 18S) rDNA and tested them on total DNAs extracted from a wide range of soils from five continents. The resulting clone libraries show mostly dictyostelid sequences (∼90%), and phylogenetic analyses of these sequences indicate novel lineages in all four dictyostelid families and most genera. This is especially true for the species-rich Heterostelium and Dictyosteliaceae but also the less species-rich Raperosteliaceae. However, the most novel deep branches are found in two very species-poor taxa, including the deepest branch yet seen in the highly divergent Cavenderiaceae. These results confirm a deep hidden diversity of Dictyostelia, potentially including novel morphologies and developmental schemes. The primers and protocols presented here should also enable more comprehensive studies of dictyostelid ecology.

Keywords
Dictyostelids, metagenetics, environmental PCR, biodiversity, biogeography
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-351108 (URN)10.1016/j.protis.2017.12.005 (DOI)000427418800006 ()29427837 (PubMedID)
Available from: 2018-05-25 Created: 2018-05-25 Last updated: 2019-08-28Bibliographically approved
Sheikh, S., Thulin, M., Cavender, J. C., Escalante, R., Kawakami, S., Lado, C., . . . Baldauf, S. L. (2018). A New Classification of the Dictyostelids. Protist, 169(1), 1-28
Open this publication in new window or tab >>A New Classification of the Dictyostelids
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2018 (English)In: Protist, ISSN 1434-4610, E-ISSN 1618-0941, Vol. 169, no 1, p. 1-28Article in journal (Refereed) Published
Abstract [en]

Traditional morphology-based taxonomy of dictyostelids is rejected by molecular phylogeny. A new classification is presented based on monophyletic entities with consistent and strong molecular phylogenetic support and that are, as far as possible, morphologically recognizable. All newly named clades are diagnosed with small subunit ribosomal RNA (18S rRNA) sequence signatures plus morphological synapomorphies where possible. The two major molecular clades are given the rank of order, as Acytosteliales ord. nov. and Dictyosteliales. The two major clades within each of these orders are recognized and given the rank of family as, respectively, Acytosteliaceae and Cavenderiaceae fam. nov. in Acytosteliales, and Dictyosteliaceae and Raperosteliaceae fam. nov. in Dictyosteliales. Twelve genera are recognized: Cavenderia gen. nov. in Cavenderiaceae, Acytostelium, Rostrostelium gen. nov. and Heterostelium gen. nov. in Acytosteliaceae, Tieghemostelium gen. nov., Hagiwaraea gen. nov., Raperostelium gen. nov. and Speleostelium gen. nov. in Raperosteliaceae, and Dictyostelium and Polysphondylium in Dictyosteliaceae. The “polycephalum” complex is treated as Coremiostelium gen. nov. (not assigned to family) and the “polycarpum” complex as Synstelium gen. nov. (not assigned to order and family). Coenonia, which may not be a dictyostelid, is treated as a genus incertae sedis. Eighty-eight new combinations are made at species and variety level, and Dictyostelium ammophilum is validated.

Keywords
Classification, dictyostelids, molecular characters, nomenclature, phylogeny, taxonomy
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-320430 (URN)10.1016/j.protis.2017.11.001 (DOI)000427418800002 ()29367151 (PubMedID)
Available from: 2017-04-20 Created: 2017-04-20 Last updated: 2019-08-28Bibliographically approved
Cavender, J. C., Vadell, E., Landolt, J. C., Stephenson, S. L., Baldauf, S. L., Roux, J., . . . Winsett, K. E. (2018). New dictyostelid cellular slime molds from South Africa. Phytotaxa, 383(3), 233-251
Open this publication in new window or tab >>New dictyostelid cellular slime molds from South Africa
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2018 (English)In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 383, no 3, p. 233-251Article in journal (Refereed) Published
Abstract [en]

A distributional study of the dictyostelid cellular slime molds (dictyostelids) of South Africa was carried out during 2006 as part of the Global Biodiversity of Eumycetozoans project based at the University of Arkansas and funded by the National Science Foundation Samples of soil/humus collected from 31 study sites yielded a total of 881 clones, with an average density of 210 clones/gram for all samples in which dictyostelids were detected. Eighteen different species were represented by one or more clones, and six of these could not be identified. These six species are described herein as new to science. In addition, information is provided on the ecological distribution of all of the species of dictyostelids now known to occur in South Africa.

Place, publisher, year, edition, pages
MAGNOLIA PRESS, 2018
Keywords
biogeography, ecological distribution, soil microhabitat, undescribed species
National Category
Biological Systematics
Identifiers
urn:nbn:se:uu:diva-372890 (URN)10.11646/phytotaxa.383.3.1 (DOI)000453537700001 ()
Available from: 2019-01-09 Created: 2019-01-09 Last updated: 2019-08-28Bibliographically approved
Urbina, H., Breed, M. F., Zhao, W., Gurrala, K. L., Andersson, S. G. .., Ågren, J., . . . Rosling, A. (2018). Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere. Fungal Biology, 122(4), 231-240
Open this publication in new window or tab >>Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere
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2018 (English)In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 122, no 4, p. 231-240Article in journal (Refereed) Published
Abstract [en]

Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endo-sphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.

Keywords
Arabidopsis, Archaeorhizomcyetes, Brassicaceae, Ion Torrent, ITS metabarcoding, Rhizosphere
National Category
Botany
Identifiers
urn:nbn:se:uu:diva-354246 (URN)10.1016/j.funbio.2017.12.013 (DOI)000430773300005 ()29551197 (PubMedID)
Funder
Swedish Research Council, 349-2007-8731Swedish Research Council, 2012-3950Australian Research Council, DE150100542Australian Research Council, DP150103414
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2018-06-19 Created: 2018-06-19 Last updated: 2019-08-28Bibliographically approved
Lidén, M., Morrison, D. A. & Baldauf, S. (Eds.). (2016). Contributions to Botany: Dedicated to Inga Hedberg. Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Contributions to Botany: Dedicated to Inga Hedberg
2016 (English)Collection (editor) (Other academic)
Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016
Series
Symbolae botanicae Upsalienses, ISSN 0082-0644 ; 38
National Category
Botany
Identifiers
urn:nbn:se:uu:diva-302478 (URN)9789155496081 (ISBN)
Available from: 2016-09-05 Created: 2016-09-05 Last updated: 2019-08-28Bibliographically approved
He, D., Fu, C.-J. & Baldauf, S. (2016). Multiple Origins of Eukaryotic cox15 Suggest Horizontal Gene Transfer from Bacteria to Jakobid Mitochondrial DNA. Molecular biology and evolution, 33(1), 122-133
Open this publication in new window or tab >>Multiple Origins of Eukaryotic cox15 Suggest Horizontal Gene Transfer from Bacteria to Jakobid Mitochondrial DNA
2016 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 1, p. 122-133Article in journal (Refereed) Published
Abstract [en]

The most gene-rich and bacterial-like mitochondrial genomes known are those of Jakobida (Excavata). Of these, the most extreme example to date is the Andalucia godoyi mitochondrial DNA (mtDNA), including a cox15gene encoding the respiratory enzyme heme A synthase (HAS), which is nuclear-encoded in nearly all other mitochondriate eukaryotes. Thuscox15 in eukaryotes appears to be a classic example of mitochondrion-to-nucleus (endosymbiotic) gene transfer, with A. godoyi uniquely retaining the ancestral state. However, our analyses reveal two highly distinct HAS types (encoded by cox15-1 and cox15-2 genes) and identifyA. godoyi mitochondrial cox15-encoded HAS as type-1 and all other eukaryotic cox15-encoded HAS as type-2. Molecular phylogeny places the two HAS types in widely separated clades with eukaryotic type-2 HAS clustering with the bulk of α-proteobacteria (>670 sequences), whereas A. godoyi type-1 HAS clusters with an eclectic set of bacteria and archaea including two α-proteobacteria missing from the type-2 clade. This wide phylogenetic separation of the two HAS types is reinforced by unique features of their predicted protein structures. Meanwhile, RNA-sequencing and genomic analyses fail to detect either cox15 type in the nuclear genome of any jakobid including A. godoyi. This suggests that not only iscox15-1 a relatively recent acquisition unique to the Andalucia lineage but also the jakobid last common ancestor probably lacked both cox15 types. These results indicate that uptake of foreign genes by mtDNA is more taxonomically widespread than previously thought. They also caution against the assumption that all α-proteobacterial-like features of eukaryotes are ancient remnants of endosymbiosis.

Place, publisher, year, edition, pages
Oxford University Press, 2016
Keywords
Horizontal gene transfer; Lateral gene transfer; Jakobid; Mitochondria; Heme A synthase
National Category
Evolutionary Biology Biochemistry and Molecular Biology Bioinformatics (Computational Biology)
Research subject
Biology with specialization in Molecular Evolution
Identifiers
urn:nbn:se:uu:diva-263178 (URN)10.1093/molbev/msv201 (DOI)000369992600009 ()26412445 (PubMedID)
Funder
Swedish Research Council
Available from: 2016-01-01 Created: 2015-09-28 Last updated: 2019-08-28Bibliographically approved
He, D., Sierra, R., Pawlowski, J. & Baldauf, S. (2016). Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria. Molecular Phylogenetics and Evolution, 101, 1-7
Open this publication in new window or tab >>Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria
2016 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 101, p. 1-7Article in journal (Refereed) Published
Abstract [en]

Rhizaria is a major eukaryotic group of tremendous diversity, including amoebae with spectacular skele- tons or tests (Radiolaria and Foraminifera), plasmodial parasites (Plasmodiophorida) and secondary endosymbionts (Chlorarachniophyta). Current phylogeny places Rhizaria in an unresolved trichotomy with Stramenopila and Alveolata (supergroup ‘‘SAR”). We assembled a 147-protein data set with exten- sive rhizarian coverage (M147), including the first transcriptomic data for a euglyphid amoeba. Phylogenetic pre-screening of individual proteins indicated potential problems with radically misplaced sequences due either to contamination of rhizarian sequences amplified from wild collected material and/or extremely long branches (xLBs). Therefore, two data subsets were extracted containing either all proteins consistently recovering rhizarian monophyly (M34) or excluding all proteins with P3 xLBs (defined as P2? the average terminal branch length for the tree). Phylogenetic analyses of M147 give conflicting results depending on the outgroup and method of analysis but strongly support an exclusive Rhizaria + Alveolata (R + A) clade with both data subsets (M34 and M37) regardless of phylogenetic method used. Support for an R + A clade is most consistent when a close outgroup is used and decreases with more distant outgroups, suggesting that support for alternative SAR topologies may reflect a long-branch attraction artifact. A survey of xLB distribution among taxa and protein functional category indicates that small ‘‘informational” proteins in particular have highly variable evolutionary rates with no consistent pattern among taxa.

Place, publisher, year, edition, pages
Elsevier, 2016
Keywords
SAR, Rhizaria, Phylogenomics, Eukaryote phylogeny
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Organismal Biology
Identifiers
urn:nbn:se:uu:diva-292712 (URN)10.1016/j.ympev.2016.04.033 (DOI)000378188100001 ()27132173 (PubMedID)
Funder
Swedish Research Council
Available from: 2016-05-08 Created: 2016-05-08 Last updated: 2019-08-28Bibliographically approved
Sheikh, S., Glöeckner, G., Kuwayama, H., Schaap, P., Urushihara, H. & Baldauf, S. L. (2015). Root of Dictyostelia based on 213 universal proteins. Molecular Phylogenetics and Evolution, 92, 53-62
Open this publication in new window or tab >>Root of Dictyostelia based on 213 universal proteins
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2015 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 92, p. 53-62Article in journal (Refereed) Published
Abstract [en]

Dictyostelia are common soil microbes that can aggregate when starved to form multicellular fruiting bodies, a characteristic that has also led to their long history of study and widespread use as model systems. Ribosomal RNA phylogeny of Dictyostelia identified four major divisions (Groups 1–4), none of which correspond to traditional genera. Group 1 was also tentatively identified as sister lineage to the other three Groups, although not consistently or with strong support. We tested the dictyostelid root using universal protein-coding genes identified by exhaustive comparison of six completely sequenced dictyostelid genomes, which include representatives of all four major molecular Groups. A set of 213 genes are low-copy number in all genomes, present in at least one amoebozoan outgroup taxon (Acanthamoeba castellanii or Physarum polycephalum), and phylogenetically congruent. Phylogenetic analysis of a concatenation of the deduced protein sequences produces a single topology dividing Dictyostelia into two major divisions: Groups 1 + 2 and Groups 3 + 4. All clades in the tree are fully supported by maximum likelihood and Bayesian inference, and all alternative roots are unambiguously rejected by the approximately unbiased (AU) test. The 1 + 2, 3 + 4 root is also fully supported even after deleting clusters with strong individual support for this root, or concatenating all clusters with low support for alternative roots. The 213 putatively ancestral amoebozoan proteins encode a wide variety of functions including 21 KOG categories out of a total of 25. These comprehensive analyses and consistent results indicate that it is time for full taxonomic revision of Dictyostelia, which will also enable more effective exploitation.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-320243 (URN)10.1016/j.ympev.2015.05.017 (DOI)000362381700005 ()26048704 (PubMedID)
Available from: 2017-04-18 Created: 2017-04-18 Last updated: 2019-08-28Bibliographically approved
He, D., Fiz-Palacios, O., Fu, C.-J., Fehling, J., Tsai, C.-C. & Baldauf, S. L. (2014). An Alternative Root for the Eukaryote Tree of Life. Current Biology, 24(4), 465-470
Open this publication in new window or tab >>An Alternative Root for the Eukaryote Tree of Life
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2014 (English)In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 24, no 4, p. 465-470Article in journal (Refereed) Published
Abstract [en]

The root of the eukaryote tree of life defines some of the most fundamental relationships among species. It is also critical for defining the last eukaryote common ancestor (LECA), the shared heritage of all extant species. The unikont-bikont root has been the reigning paradigm for eukaryotes for more than 10 years but is becoming increasingly controversial. We developed a carefully vetted data set, consisting of 37 nuclear-encoded proteins of close bacterial ancestry (euBacs) and their closest bacterial relatives, augmented by deep sequencing of the Acrasis kona (Heterolobosea, Discoba) transcriptome. Phylogenetic analysis of these data produces a highly robust, fully resolved global phy- logeny of eukaryotes. The tree sorts all examined eukaryotes into three megagroups and identifies the Discoba, and potentially its parent taxon Excavata, as the sister group to the bulk of known eukaryote diversity, the proposed Neozoa (Amorphea + Stramenopila+Alveolata+Rhizaria+ Plantae [SARP]). All major alternative hypotheses are rejected with as little as w50% of the data, and this resolu- tion is unaffected by the presence of fast-evolving alignment positions or distant outgroup sequences. This ‘‘neozoan- excavate’’ root revises hypotheses of early eukaryote evolution and highlights the importance of the poorly stud- ied Discoba for understanding the evolution of eukaryotic diversity and basic cellular processes. 

Keywords
Eukaryote root, molecular phylogenetics, phylogenetics
National Category
Biological Systematics Evolutionary Biology Bioinformatics (Computational Biology)
Research subject
Biology with specialization in Evolutionary Organismal Biology; Biology with specialization in Molecular Evolution; Biology with specialization in Systematics
Identifiers
urn:nbn:se:uu:diva-218740 (URN)10.1016/j.cub.2014.01.036 (DOI)000331718900032 ()
Funder
Swedish Research Council
Available from: 2014-02-16 Created: 2014-02-16 Last updated: 2019-08-28Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0003-4485-6671

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