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  • 101. Farah, Mohamed
    et al.
    Olsson, Sten
    Bate, Jenny
    Lindquist, Marie
    Edwards, Ralph
    Simmonds, Monique
    Leon, Christine
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Botanical Nomenclature in Pharmacovigilance and a Recommendation for Standardisation2006In: Drug Safety, ISSN 0114-5916, Vol. 29, p. 1023-1029Article in journal (Refereed)
    Abstract [en]

    Nomenclature of plants in pharmacology can be presented by pharmaceutical

    names or scientific names in the form of Linnaean binomials. In this paper,

    positive and negative aspects of both systems are discussed in the context of the

    scientific nomenclatural framework and the systems’ practical applicability. The

    Uppsala Monitoring Centre (UMC) runs the WHO Programme for International

    Drug Monitoring and is responsible for the WHO Adverse Drug Reaction (ADR)

    database that currently contains 3.6 million records WHO Adverse Drug Reaction

    database. In order for the UMC to monitor pharmacovigilance through ADRs to

    herbal medicine products the following species nomenclatural criteria are important:

    (i) the name should indicate only one species of plant; (ii) the source for this

    name must be authoritative; (iii) the name should indicate which part of the plant

    is used. Based on these criteria, the UMC investigated four options: (i) adopt main

    names used in recognised (inter-) national pharmacopoeias or authoritative publications;

    (ii) adopt option 1, but cite the publication for all names in abbreviated

    form; (iii) three-part pharmaceutical names consisting of Latinised part name plus

    Latinised genus name, plus Latinised specific epithet; (iv) scientific binomial

    names, optionally with author and plant part used. The UMC has selectedchosen

    for the latter option and willas its adoption utilizes the scientific botanical

    nomenclature as defined by the International Code of Botanical Nomenclature.

  • 102.
    Farah, Mohamed
    et al.
    Uppsala Monitoring Centre.
    Olsson, Sten
    Uppsala Monitoring Centre.
    Bate, Jenny
    Uppsala Monitoring Centre.
    Lindquist, Marie
    Uppsala Monitoring Centre.
    Edwards, Ralph
    Uppsala Monitoring Centre.
    Simmonds, Monique
    Royal Botanic Gardens Kew.
    Leon, Christine
    Royal Botanic Gardens Kew.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Botanical Nomenclature in Pharmacovigilance and a Recommendation for Standardisation2006In: Drug Safety, ISSN 0114-5916, E-ISSN 1179-1942, Vol. 29, no 11, p. 1023-1029Article in journal (Refereed)
    Abstract [en]

    Nomenclature of plants in pharmacology can be presented by pharmaceutical names or scientific names in the form of Linnaean binomials. In this paper, positive and negative aspects of both systems are discussed in the context of the scientific nomenclatural framework and the systems' practical applicability. The Uppsala Monitoring Centre (UMC) runs the WHO Programme for International Drug Monitoring and is responsible for the WHO Adverse Drug Reaction (ADR) database that currently contains 3.6 million records. In order for the UMC to monitor pharmacovigilance through ADRs to herbal medicine products the following nomenclatural criteria are important: (i) the name should indicate only one species of plant; (ii) the source for this name must be authoritative; (iii) the name should indicate which part of the plant is used. Based on these criteria, the UMC investigated four options: (i) adopt main names used in recognised (inter-) national pharmacopoeias or authoritative publications; (ii) adopt option 1, but cite the publication for all names in abbreviated form; (iii) three-part pharmaceutical names consisting of Latinised part name plus Latinised genus name, plus Latinised specific epithet; (iv) scientific binomial names, optionally with author and plant part used. The UMC has chosen the latter option and will at its adoption utilise the scientific botanical nomenclature as defined by the International Code of Botanical Nomenclature. This decision satisfies all criteria set by the UMC and renders the necessity of creating a new system or upgrading an old inconsistent system obsolete. The UMC has also issued an extensive synonymy checklist of vernacular, pharmaceutical and scientific names for the herbals in the WHO ADR database. We strongly recommend the adoption of scientific names to denote plant ingredients in medicine.

  • 103.
    Farida, Seyed Hamed Moazzami
    et al.
    Bu Ali Sina Univ, Dept Biol, Fac Sci, Hamadan, Iran.
    Ghorbani, Abdolbaset
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Shahid Beheshti Univ Med Sci, Tradit Med & Mat Med Res Ctr, Tehran, Iran.
    Ajani, Yousef
    IBRC, Plant Bank, Karaj, Iran.
    Sadr, Mohammad
    Encyclopedia Islamica Res Ctr, Hist Sci, Tehran, Iran.
    Mozaffarian, Valiollah
    Res Inst Forests & Rangelands, Tehran, Iran.
    Ethnobotanical Applications and Their Correspondence with Phylogeny in Apiaceae-Apioideae2018In: RESEARCH JOURNAL OF PHARMACOGNOSY, ISSN 2345-5977, Vol. 5, no 3, p. 79-97Article, review/survey (Refereed)
    Abstract [en]

    The Apiaceae family includes some of the most known medicinal, food and spice species in the world some of which have been used by humans since antiquity. Local people in different regions use many species of the family but the information regarding their uses is scattered. Traditionally used species are good candidates for bioprospecting. Combining traditional uses with phylogenetic data helps in selecting species for bioprospecting. In the present study, an ethnobotanical literature review was conducted to outline a comprehensive overview of the ethnobotanical importance of the family in Iran. To highlight the most ethnobotanically used groups in the family, ethnobotanical data were overlapped with generic phylogeny tree of the subfamily Apioideae. In total, 72 species (17.27%) from 42 genera (33.87%) were found to have ethnobotanical uses. Main uses of the family members were medicinal purposes (67.30%) followed by culinary (25%) and ethnoveterinary (11.11%) uses. Two categories of potential species groups for further bioprospecting investigations have been identified based on the phylogenetic analysis. Based on the findings of the present study, phylogenetic analysis can help in identifying potential groups for bioprospecting studies. More rigorous phylogenetic analysis that combines chemotaxonomy data, ethnomedicinal data and phylogenetic data are necessary to pinpoint exact lineages for specific medicinal properties.

  • 104.
    Farida, Seyed Hamed Moazzami
    et al.
    Shahed Univ, Dept Biol, Fac Basic Sci, Tehran 3319118651, Iran..
    Radjabian, Tayebeh
    Shahed Univ, Dept Biol, Fac Basic Sci, Tehran 3319118651, Iran..
    Ranjbar, Massoud
    Bu Ali Sina Univ, Dept Biol, Fac Sci, Hamadan 651754161, Iran..
    Salami, Seyed Alireza
    Univ Tehran, Dept Hort Sci, Fac Agr Sci & Engn, Coll Agr & Nat Resources, Karaj 3158777871, Iran..
    Rahmani, Nosrat
    Shahed Univ, Dept Biol, Fac Basic Sci, Tehran 3319118651, Iran..
    Ghorbani, Abdolbaset
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fatty Acid Patterns of Seeds of Some Salvia Species from Iran: A Chemotaxonomic Approach2016In: Chemistry and Biodiversity, ISSN 1612-1872, E-ISSN 1612-1880, Vol. 13, no 4, p. 451-458Article in journal (Refereed)
    Abstract [en]

    In this study, the seed oil content and fatty acid (FA) profile of 21 populations from 16 wild Salvia species of Iran were analyzed by GC. Patterns of chemical variations of the oils among species were identified via numerical analyses and also the taxonomic status of the infrageneric grouping was outlined in the genus. Salvia species were scored based on the contents of main FAs using principal coordinate analysis (PCO). The results showed that the total oil content in the seeds varied significantly, and ranged from 6.68 to 38.53% dry weight. alpha-Linolenic (18:3 omega 3, 1.69 -53.56%), linoleic (18:2 omega 6, 13.04 - 60.64%), oleic (18:1 omega 9, 6.15 - 27.06%), palmitic (16:0, 3.77-9.27%), and stearic (18:0, 1.78 - 3.05%) acid were identified as five major FAs in the oils. The amount of omega-3 and omega-6 FAs ranged between 1.90 - 53.80% and 13.46 - 60.83% of total FAs in the seed oils, respectively. The results confirmed that FA profiles were distinctive among the species and that they can be used as chemotaxonomic markers. The discrimination of Salvia species according to their botanical classification at intersectional level was supported. In general, seed oils of Salvia species were rich sources of polyunsaturated FAs, except in linoleic and alpha-linolenic acid, and may be valuable for food and pharmaceutical industries.

  • 105.
    Fehling, Johanna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Davidson, Keith
    Bolch, Christopher J. S.
    Brand, Tim D.
    Narayanaswamy, Bhavani E.
    The Relationship between Phytoplankton Distribution and Water Column Characteristics in North West European Shelf Sea Waters2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 3, p. e34098-Article in journal (Refereed)
    Abstract [en]

    Phytoplankton underpin the marine food web in shelf seas, with some species having properties that are harmful to human health and coastal aquaculture. Pressures such as climate change and anthropogenic nutrient input are hypothesized to influence phytoplankton community composition and distribution. Yet the primary environmental drivers in shelf seas are poorly understood. To begin to address this in North Western European waters, the phytoplankton community composition was assessed in light of measured physical and chemical drivers during the "Ellett Line" cruise of autumn 2001 across the Scottish Continental shelf and into adjacent open Atlantic waters. Spatial variability existed in both phytoplankton and environmental conditions, with clear differences not only between on and off shelf stations but also between different on shelf locations. Temperature/salinity plots demonstrated different water masses existed in the region. In turn, principal component analysis (PCA), of the measured environmental conditions (temperature, salinity, water density and inorganic nutrient concentrations) clearly discriminated between shelf and oceanic stations on the basis of DIN:DSi ratio that was correlated with both salinity and temperature. Discrimination between shelf stations was also related to this ratio, but also the concentration of DIN and DSi. The phytoplankton community was diatom dominated, with multidimensional scaling (MDS) demonstrating spatial variability in its composition. Redundancy analysis (RDA) was used to investigate the link between environment and the phytoplankton community. This demonstrated a significant relationship between community composition and water mass as indexed by salinity (whole community), and both salinity and DIN: DSi (diatoms alone). Diatoms of the Pseudo-nitzschia seriata group occurred at densities potentially harmful to shellfish aquaculture, with the potential for toxicity being elevated by the likelihood of DSi limitation of growth at most stations and depths.

  • 106.
    Ferm, Julia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A preliminary phylogeny of Zapoteca (Fabaceae: Caesalpinioideae: Mimosoid clade)2019In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 305, no 5, p. 341-352Article in journal (Refereed)
    Abstract [en]

    The legume genus Zapoteca is separated from the genus Calliandra, i.e., by having pollen arranged in 16-grained polyads (compared to 8-grained polyads in Calliandra) and in chromosome number (13 vs. 8 or 11). As currently circumscribed, Zapoteca contains 22 species and 13 subspecies placed in five subgenera. This study included 20 species and 11 subspecies representing all subgenera. Representative species from the closely related genera Calliandra, Havardia, Pithecellobium and Viguieranthus were also included, as the more distantly related species Senegalia senegal and Vachellia farnesiana. The aims of this study were to test the monophyly of Zapoteca and investigate phylogenetic relationships within the genus. Total DNA was extracted from leaf material and the nuclear ETS and ITS, and plastid trnL-trnF regions were amplified. Additional sequence data were downloaded from GenBank, and the data sets were analyzed using Bayesian inference. Results show that Zapoteca is monophyletic and that the monospecific subgenera (subg. Nervosa and subg. Aculeata) are resolved as separate lineages within the genus, subg. Nervosa (containing Z. nervosa) as sister to all remaining taxa of Zapoteca. Subgenera containing more than one species (subg. Amazonica, subg. Zapoteca and subg. Ravenia) are shown to be non-monophyletic. Two subspecies of Z. caracasana, subsp. caracasana and subsp. weberbaueri, are found together in a clade. Furthermore, Zapoteca tehuana and Z. portoricensis subsp. portoricensis, Z. formosa subsp. gracilis and Z. formosa subsp. schottii are shown to be monophyletic. However, the other subspecific taxa of Z. formosa and of Z. portoricensis are not supported as monophyletic.

  • 107.
    Ferm, Julia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Stockholm Univ, Dept Bot, SE-10691 Stockholm, Sweden.
    Kårehed, Jesper
    Uppsala University, Music and Museums, The Linnean Gardens of Uppsala.
    Bremer, Birgitta
    Stockholm Univ, Dept Bot, SE-10691 Stockholm, Sweden; Royal Swedish Acad Sci, Bergius Fdn, SE-10405 Stockholm, Sweden.
    Razafimandimbison, Sylvain G
    Royal Swedish Acad Sci, Bergius Fdn, SE-10405 Stockholm, Sweden; Swedish Museum Nat Hist, Dept Bot, Box 50007, SE-10405 Stockholm, Sweden.
    Paracarphalea, a new genus of the coffee family segregated from the Malagasy endemic genus Carphalea (Rubiaceae, Rubioideae, Knoxieae)2016In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 263, no 2, p. 98-112Article in journal (Refereed)
    Abstract [en]

    The Malagasy genus Carphalea (Rubiaceae) consists of six species (C. angulata, C. cloiselii, C. kirondron, C. linearifolia, C. madagascariensis, C. pervilleana) of shrubs or small trees and is recognizable by a distinctly lobed calyx, 2(–4)-locular ovaries, each locule with several ovules on a rod-like stalk arising from the base of the locule, and indehiscent fruits. Carphalea linearifolia, rediscovered in 2010, has not previously been included in any Rubiaceae molecular phylogenetic studies. We re-investigated the monophyly of Carphalea using sequence data from chloroplast (rps16 and trnT-F) and nuclear (ITS and ETS) markers analysed with parsimony and Bayesian methods. Carphalea linearifolia forms a clade with Ccloiselii and the type species C. madagascariensis. This clade is sister to a clade consisting of the rest of the Carphalea species plus the genus Triainolepis. According to these results, the new genus Paracarphalea is here described to accommodate Carphalea angulata, C. kirondron, and C. pervilleana. Theconservation status of Carphalea linearifolia is assessed as critically endangered according to IUCN criteria.

  • 108. Field, Dawn
    et al.
    Garrity, George
    Gray, Tanya
    Morrison, Norman
    Selengut, Jeremy
    Sterk, Peter
    Tatusova, Tatiana
    Thomson, Nicholas
    Allen, Michael J
    Angiuoli, Samuel V
    Ashburner, Michael
    Axelrod, Nelson
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Ballard, Stuart
    Boore, Jeffrey
    Cochrane, Guy
    Cole, James
    Dawyndt, Peter
    De Vos, Paul
    DePamphilis, Claude
    Edwards, Robert
    Faruque, Nadeem
    Feldman, Robert
    Gilbert, Jack
    Gilna, Paul
    Glöckner, Frank Oliver
    Goldstein, Philip
    Guralnick, Robert
    Haft, Dan
    Hancock, David
    Hermjakob, Henning
    Hertz-Fowler, Christiane
    Hugenholtz, Phil
    Joint, Ian
    Kagan, Leonid
    Kane, Matthew
    Kennedy, Jessie
    Kowalchuk, George
    Kottmann, Renzo
    Kolker, Eugene
    Kravitz, Saul
    Kyrpides, Nikos
    Leebens-Mack, Jim
    Lewis, Suzanna E
    Li, Kelvin
    Lister, Allyson L
    Lord, Phillip
    Maltsev, Natalia
    Markowitz, Victor
    Martiny, Jennifer
    Methe, Barbara
    Mizrachi, Ilene
    Moxon, Richard
    Nelson, Karen
    Parkhill, Julian
    Proctor, Lita
    White, Owen
    Sansone, Susanna-Assunta
    Spiers, Andrew
    Stevens, Robert
    Swift, Paul
    Taylor, Chris
    Tateno, Yoshio
    Tett, Adrian
    Turner, Sarah
    Ussery, David
    Vaughan, Bob
    Ward, Naomi
    Whetzel, Trish
    San Gil, Ingio
    Wilson, Gareth
    Wipat, Anil
    The minimum information about a genome sequence (MIGS) specification.2008In: Nature biotechnology, ISSN 1546-1696, Vol. 26, no 5, p. 541-7Article in journal (Refereed)
    Abstract [en]

    With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.

  • 109.
    Fiz-Palacios, Omar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ahmadzadeh, Afsaneh
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Weststrand, Stina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ahlberg, Per Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Did terrestrial diversification of amoebas (Amoebozoa) occur in synchrony with land plants?2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 9, p. e74374-Article in journal (Refereed)
    Abstract [en]

    Evolution of lineage diversification through time is an active area of research where much progress has been made in the last decade. Contrary to the situation in animals and plants little is known about how diversification rates have evolved in most major groups of protist. This is mainly due to uncertainty about phylogenetic relationships, scarcity of the protist fossil record and the unknown diversity within these lineages. We have analyzed the evolutionary history of the supergroup Amoebozoa over the last 1000 million years using molecular dating and species number estimates. After an origin in the marine environment we have dated the colonization of terrestrial habitats by three distinct lineages of Amoebozoa: Dictyostelia, Myxogastria and Arcellinida. The common ancestor of the two sister taxa, Dictyostelia and Myxogastria, appears to have existed before the colonization of land by plants. In contrast Arcellinida seems to have diversify in synchrony with land plant radiation, and more specifically with that of mosses. Detection of acceleration of diversification rates in Myxogastria and Arcellinida points to a co-evolution within the terrestrial habitats, where land plants and the amoebozoans may have interacted during the evolution of these new ecosystems.

  • 110.
    Fiz-Palacios, Omar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Schneider, Harald
    Heinrichs, Jochen
    Savolainen, Vincent
    Diversification of land plants: insights from a family-level phylogenetic analysis2011In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 11, p. 341-Article in journal (Refereed)
    Abstract [en]

    Background: Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. Results: We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. Conclusions: This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.

  • 111.
    Fiz-Palacios, Omar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Valcarcel, Virginia
    From Messinian crisis to Mediterranean climate: A temporal gap of diversification recovered from multiple plant phylogenies2013In: Perspectives in plant ecology, evolution and systematics, ISSN 1433-8319, E-ISSN 1618-0437, Vol. 15, no 2, p. 130-137Article in journal (Refereed)
    Abstract [en]

    Paleobotanical and molecular studies link diversification of plants in the Mediterranean Basin with the onset of the Mediterranean climate. Screening diversification before this period is needed in order to analyze whether the observed increase in diversification is a legitimate footprint denoting radiation or instead the biological signal of a previous mass extinction or rate stasis period. A shared post-Messinian temporal gap of cladogenesis has been previously observed in two Mediterranean sister genera. Based on this evidence we explored recently published molecular studies to recover lineages with similar diversification profiles exhibiting a cladogenesis gap. Using this criterion, we conducted a meta-analysis of 36 Mediterranean plant lineages with a post-Messinian temporal gap of cladogenesis, including a new molecular dating of Genista (Fabaceae). Whereas 39% of these lineages have not diversified since the Miocene, another 39% began to rediversify during the onset of the Mediterranean climate and the remaining 22% began diversifying again afterwards during the Quaternary. The pattern of Mediterranean diversification recovery after a temporal gap of cladogenesis was also obtained with phylogenetic tree simulations under birth and death processes when forcing one or two temporal shifts in diversification rates. The relative importance of the Mediterranean onset as a driving force promoting speciation or triggering extinction remains as an open question, since neither the mass extinction nor the rate stasis evolutionary scenarios can be rule out. The independent analysis of individual clades within phylogenies is also essential to detect clade-dependent patterns hidden by phylogeny-level ones. We disclose the importance of analyzing diversification patterns of Mediterranean lineages since the Miocene to understand the recent history of the Mediterranean biota.

  • 112.
    Fiz-Palacios, Omar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Valcarcel, Virginia
    Imbalanced diversification of two Mediterranean sister genera (Bellis and Bellium, Asteraceae) within the same time frame2011In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 295, no 1-4, p. 109-118Article in journal (Refereed)
    Abstract [en]

    The Daisies, Bellis and Bellium, form a monophyletic complex within the core Astereae (Asteraceae). Although most early diverging lineages show an African distribution, the core Astereae is today widespread on five continents with the Bellis/Bellium complex as the only representative in the Mediterranean basin. Molecular clock estimates placed the divergence of Astereae from its sister tribe Anthemideae in the Oligocene. Using a combination of three plastid genes, we estimated divergence times for different lineages of the tribe Astereae. This, together with temporal and biogeographical reconstructions using the nrITS region, allows placing and timing of the major lineages of the Bellis/Bellium complex. The age reconstruction places the divergence of the tribe Astereae in the late Miocene (18-19 million years ago), followed by an out-of-Africa dispersal into Asia where the worldwide expansion may have started. Our results suggest that the colonization of the Mediterranean basin by the Astereae started from Eurasia some 10 million years ago. A Messinian early divergence of the Bellis/Bellium complex in the Mediterranean was estimated. However, a parallel 4-million-year delay for the within-genera diversification was inferred, probably related to the establishment of the sclerophyllous Mediterranean forest. Despite a similar time frame for the within-genera diversification, today's species numbers differ considerably between Bellis (15 spp.) and Bellium (five spp.).

  • 113.
    Fiz-Palacios, Omar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Vargas, Pablo
    Vila, Roger
    Papadopulos, Alexander S. T.
    Aldasoro, Juan José
    The uneven phylogeny and biogeography of Erodium (Geraniaceae): radiations in the Mediterranean and recent recurrent intercontinental colonization2010In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 106, no 6, p. 871-884Article in journal (Refereed)
    Abstract [en]

    Background and Aims: The genus Erodium is a common feature of Mediterranean-type climates throughout the world, but the Mediterranean Basin has significantly higher diversity than other areas. The aim here is to reveal the biogeographical history of the genus and the causes behind the evolution of the uneven distribution. Methods Seventy-eight new nrITS sequences were incorporated with existing plastid data to explore the phylogenetic relationships and biogeography of Erodium using several reconstruction methods. Divergence times for major clades were calculated and contrasted with other previously published information. Furthermore, topological and temporal diversification rate shift analyses were employed using these data. Key Results Phylogenetic relationships among species are widely congruent with previous plastid reconstructions, which refute the classical taxonomical classification. Biogeographical reconstructions point to Asia as the ancestral area of Erodium, arising approx. 18 MYA. Four incidences of intercontinental dispersal from the Mediterranean Basin to similar climates are demonstrated. Increases in diversification were present in two independent Erodium lineages concurrently. Two bursts of diversification (3 MYA and 0·69 MYA) were detected only in the Mediterranean flora.Conclusions Two lineages diverged early in the evolution of the genus Erodium: (1) subgenus Erodium plus subgenus Barbata subsection Absinthioidea and (2) the remainder of subgenus Barbata. Dispersal across major water bodies, although uncommon, has had a major influence on the distribution of this genus and is likely to have played as significant role as in other, more easily dispersed, genera. Establishment of Mediterranean climates has facilitated the spread of the genus and been crucial in its diversification. Two, independent, rapid radiations in response to the onset of drought and glacial climate change indicate putative adaptive radiations in the genus.

  • 114. Frajman, Božo
    et al.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Oxelman, Bengt
    Taxonomic revision of Atocion and Viscaria (Sileneae, Caryophyllaceae)2013In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 173, no 2, p. 194-210Article in journal (Refereed)
    Abstract [en]

    A species-level taxonomic revision of Atocion and Viscaria, based on a recent phylogenetic study, is presented. Atocion includes six species (A. armeria, A. compactum, A. lerchenfeldianum, A. reuterianum, A. rupestre and A. scythicinum), and Viscaria includes three species (V. alpina, V. asterias and V. vulgaris). The highest species diversity is found on the Balkan Peninsula. Species descriptions based on a study of morphological characters and generated using the Prometheus description model are provided and are also available in the Sileneae online database. Complete synonymy, notes on the ecology and geographical distribution of the taxa and an identification key are provided. Lectotypes for nine names (Lychnis helvetica, L. suecica, Silene armeria var. angustifolia, S. berdaui, S. lituanica, S. compacta, S. orientalis, S. reuteriana and Viscaria media) and a neotype for one name (S. lerchenfeldiana) are assigned.

  • 115.
    Fu, Cheng-jie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sheikh, Sanea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Miao, Wei
    Andersson, Siv G. E.
    Baldauf, Sandra L.
    Missing Genes, Multiple ORFs, and C-to-U Type RNA Editing in Acrasis kona (Heterolobosea, Excavata) Mitochondrial DNA2014In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653Article in journal (Refereed)
  • 116.
    Fu, Cheng-Jie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sheikh, Sanea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Miao, Wei
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Missing Genes, Multiple ORFs, and C-to-U Type RNA Editing in Acrasis kona (Heterolobosea, Excavata) Mitochondrial DNA2014In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 6, no 9, p. 2240-2257Article in journal (Refereed)
    Abstract [en]

    Discoba (Excavata) is an ancient group of eukaryotes with great morphological and ecological diversity. Unlike the other major divisions of Discoba (Jakobida and Euglenozoa), little is known about the mitochondrial DNAs(mtDNAs) of Heterolobosea. We have assembled a complete mtDNA genome from the aggregating heterolobosean amoeba, Acrasis kona, which consists of a single circular highly AT-rich (83.3%) molecule of 51.5 kb. Unexpectedly, A. kona mtDNA is missing roughly 40% of the protein-coding genes and nearly half of the transfer RNAs found in the only other sequenced heterolobosean mtDNAs, those of Naegleria spp. Instead, over a quarter of A. kona mtDNA consists of novel open reading frames. Eleven of the 16 protein-coding genes missing from A. kona mtDNA were identified in its nuclear DNA and polyA RNA, and phylogenetic analyses indicate that at least 10 of these 11 putative nuclear-encoded mitochondrial (NcMt) proteins arose by direct transfer from the mitochondrion. Acrasis kona mtDNA also employs C-to-U type RNA editing, and 12 homologs of DYW-type pentatricopeptide repeat (PPR) proteins implicated in plant organellar RNA editing are found in A. kona nuclear DNA. A mapping of mitochondrial gene content onto a consensus phylogeny reveals a sporadic pattern of relative stasis and rampant gene loss in Discoba. Rampant loss occurred independently in the unique common lineage leading to Heterolobosea + Tsukubamonadida and later in the unique lineage leading to Acrasis. Meanwhile, mtDNA gene content appears to be remarkably stable in the Acrasis sister lineage leading to Naegleria and in their distant relatives Jakobida.

  • 117. Gao, Xin-Fen
    et al.
    Peng, Yu-Lan
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Wang, Ying-Wei
    Three new species of Corydalis (Fumariaceae) from northwestern Sichuan China2008In: Novon, ISSN 1055-3177, E-ISSN 1945-6174, Vol. 18, no 3, p. 330-335Article in journal (Refereed)
    Abstract [en]

    The jiuding Ridge (Sichuan, China) has been explored during the past several years by a team from chengdu Institute of Biology. Chinese Academy of Sciences, and three undescribed species of Corydalis DC. (Fumariaceae) have been revealed and are apparently endemic to this mountain. The new species were observed in forest (C. capitata X.F. Cao, Liden & Y.W. Wang), and alpine rocky limestone areas (C. schistostigma X.F. Cao, Liden, Y.W. Wang & Y.L. Peng). The two first species have their closest relatives in the Wolong-Balangshan District in the Wolong-Balangshan District (Wenchuan. Sichuan). Corydalis aeaeae differs from C. panada Liden & Y.W. Wang in its small size, few-flowered racemes, and broadly obtuse outer petals with low, short erests. Corydalis capitata differs from the C. flexuosa Franchet complex in the capitate racemes, small flowers with deeply serrate petals, and the peculiar, thin, strictly ecect lateral branches. corydalis schistostinma is unique in the C. curviflora Maximowicz ex Hemsley group, in the deeply cleft stigma and very forward-projecting crests to the inner petals, and possibly has iits affinities more to the north and northwest in the Hengduan Mountains.

  • 118. Gato-Calvo, Lucia
    et al.
    Vierna, Joaquin
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Barcoding the Trendy Sweetener Stevia2014In: iBOL Barcode Bulletin, Vol. 6, p. 6-7Article in journal (Other (popular science, discussion, etc.))
  • 119. Geiger, Jennifer M.O.
    et al.
    Korall, Petra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ranker, Tom A.
    Kleist, Annabelle C.
    Nelson, Christine L.
    Molecular phylogenetic relationships of Cibotium and origin of the Hawaiian endemics2013In: American Fern Journal, ISSN 0002-8444, E-ISSN 1938-422X, Vol. 103, no 3, p. 141-152Article in journal (Refereed)
    Abstract [en]

    The tree fern genus Cibotium comprises nine species distributed in tropical regions of Asia, Mesoamerica, and the Hawaiian Islands. The four Hawaiian species are endemic to the Hawaiian Islands. The goals of this paper were to determine the relationships among the Cibotium species, determine whether the Hawaiian species are monophyletic, and infer the dispersal pathway likely responsible for delivering an ancestral Cibotium species to the Hawaiian Islands. Molecular phylogenetic analyses based on four coding and five non-coding plastid DNA sequences supported Hawaiian Cibotium as monophyletic, suggesting a single colonization of the Hawaiian Islands. Hawaiian Cibotium are most closely related to species in Mesoamerica. If the ancestor of Hawaiian Cibotium dispersed to the Hawaiian Islands via wind dispersed spores, our analyses suggest the trade winds or storms delivered spores from Mesoamerica or the Hawaiian Islands were colonized first by a species from Asia, followed by subsequent dispersal to Mesoamerica from Hawai'i. Our analyses do not allow us to favor one hypothesis over the other.

  • 120.
    Ghorbani, Abdolbaset
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Nat Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands..
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, POB 1172, N-0318 Oslo, Norway..
    Maas, Paul J. M.
    Nat Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands..
    van Andel, Tinde
    Nat Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands.;Leiden Univ, Clusius Chair Hist Bot & Gardens, POB 9517, NL-2300 RA Leiden, Netherlands..
    The typification of two Linnaean plant names based on illustrations published by Leonhard Rauwolf in 15832017In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 66, no 5, p. 1204-1207Article in journal (Refereed)
    Abstract [en]

    Based on an assessment of the illustrations published in the travel account of Leonhard Rauwolf and the corresponding specimens collected by him between 1573 and 1575 in the Near East, lectotypes are designated for the Linnaean names Aristolochia maurorum and Rheum ribes, which have not been typified previously.

  • 121.
    Ghorbani, Abdolbaset
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Gravendeel, Barbara
    Naghibi, Farzaneh
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Wild orchid tuber collection in Iran: a wake-up call for conservation2014In: Biodiversity and Conservation, ISSN 0960-3115, E-ISSN 1572-9710, Vol. 23, no 11, p. 2749-2760Article in journal (Refereed)
    Abstract [en]

    Wild orchids are traditionally harvested as Salep and used in traditional medicine and ice-cream production in Iran. Recently however, illegal harvest of wild orchids for export appears to have grown. This study aimed to: (1) determine the diversity of harvested wild orchid species and their collection sites in Iran; and (2) study the current harvest status and trade chain and volume to estimate the total orchid plant extraction from natural populations. Field surveys of collectors and market surveys of traders were conducted to establish the diversity of collected species, to identify harvest hotspots, and to document harvesting and trade volumes. Sixteen species and subspecies from 7 genera of Orchidaceae are collected for their tubers. Based on estimates from the 2013 April to June harvest season more than 24.5 tons of fresh tubers were collected from three districts in Golestan province alone. It is estimated that this amount of tuber requires the lethal destructive harvesting of 5.5 -6.1 million orchids, with a market value of 320,000 USD. In the Tehran Bazar Salep trade during May-July 2013 was 1.9 tons of dried tubers, with estimated retail value of 310,000 USD. Current orchid collection practices in Iran, which have soared in recent years due to international demand, do not seem sustainable as all tubers are collected destructively. To preserve orchid populations, in the longterm, establishment of specific Orchid Conservation Areas and introduction of sustainable production practices, could alleviate harvesting pressure. In the midterm, development of a DNA barcoding-based molecular identification system could help to monitor and control illegal trade. In the near term, effective implementation of collection bans in excessively harvested areas and strengthening of current regulations are necessary to avoid the catastrophic effects of harvesting on orchid populations, as has been observed in Turkey.

  • 122.
    Ghorbani, Abdolbaset
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Traditional Medicine and Materia Medica Research Center, Shahid Beheshti University of Medical Sciences, No 19, Tavanir Street, Hemmat Highway, P.O. Box 14155-6153, Tehran, Iran..
    Gravendeel, Barbara
    Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.; University of Applied Sciences Leiden, Zernikedreef 11, 2333, CK Leiden, The Netherlands..
    Selliah, Sugirthini
    The Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway..
    Zarré, Shahin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Department of Plant Sciences, School of Biology, College of Science, University of Tehran, 14155-6455, Tehran, Iran..
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.; The Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway..
    DNA barcoding of tuberous Orchidoideae: a resource for identification of orchids used in Salep2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 2, p. 342-352Article in journal (Refereed)
    Abstract [en]

    Tubers of terrestrial orchids are harvested and traded from the eastern Mediterranean to the Caspian Sea for the traditional product Salep. Overexploitation of wild populations and increased middle-class prosperity have escalated prices for Salep, causing overharvesting, depletion of native populations and providing an incentive to expand harvesting to untapped areas in Iran. Limited morphological distinctiveness among traded Salep tubers renders species identification impossible, making it difficult to establish which species are targeted and affected the most. In this study, a reference database of 490 nrITS, trnL-F spacer and matK sequences of 133 taxa was used to identify 150 individual tubers from 31 batches purchased in 12 cities in Iran to assess species diversity in commerce. The sequence reference database consisted of 211 nrITS, 158 trnL-F and 121 matK sequences, including 238 new sequences from collections made for this study. The markers enabled unambiguous species identification with tree-based methods for nrITS in 67% of the tested tubers, 58% for trnL-F and 59% for matK. Species in the genera Orchis (34%), Anacamptis (27%) and Dactylorhiza (19%) were the most common in Salep. Our study shows that all tuberous orchid species in this area are threatened by this trade, and further stresses the urgency of controlling illegal harvesting and cross-border trade of Salep tubers.

  • 123.
    Ghorbani, Abdolbaset
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Saeedi, Yousef
    Shahid Beheshti Univ Med Sci, Tradit Med & Mat Med Res Ctr, Tehran, Iran..
    de Boer, Hugo J.
    Univ Oslo, Nat Hist Museum, Oslo, Norway..
    DNA barcoding in ethnobotany and ethnopharmacology: identifying medicinal plants traded in local markets2015In: Genome, ISSN 0831-2796, E-ISSN 1480-3321, Vol. 58, no 5, p. 220-220Article in journal (Other academic)
  • 124.
    Ghorbani, Abdolbaset
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Shahid Beheshti Univ Med Sci, Tradit Med & Mat Med Res Ctr, Tehran, Iran..
    Saeedi, Yousef
    Shahid Beheshti Univ Med Sci, Tradit Med & Mat Med Res Ctr, Tehran, Iran..
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Naturalis Biodivers Ctr, Leiden, Netherlands.;Univ Oslo, Nat Hist Museum, Oslo, Norway..
    Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 4, article id e0175722Article in journal (Refereed)
    Abstract [en]

    Local markets provide a rapid insight into the medicinal plants growing in a region as well as local traditional health concerns. Identification of market plant material can be challenging as plants are often sold in dried or processed forms. In this study, three approaches of DNA barcoding-based molecular identification of market samples are evaluated, two objective sequence matching approaches and an integrative approach that coalesces sequence matching with a priori and a posteriori data from other markers, morphology, ethnoclassification and species distribution. Plant samples from markets and herbal shops were identified using morphology, descriptions of local use, and vernacular names with relevant floras and pharmacopoeias. DNA barcoding was used for identification of samples that could not be identified to species level using morphology. Two methods based on BLAST similaritybased identification, were compared with an integrative identification approach. Integrative identification combining the optimized similarity-based approach with a priori and a posteriori information resulted in a 1.67, 1.95 and 2.00 fold increase for ITS, trnL-F spacer, and both combined, respectively. DNA barcoding of traded plant material requires objective strategies to include data from multiple markers, morphology, and traditional knowledge to optimize species level identification success.

  • 125.
    Ghorbani, Abdolbaset
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Naturalis Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands.
    Wieringa, Jan J.
    Naturalis Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Naturalis Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands; Univ Oslo, Nat Hist Museum, POB 1172 Blindern, N-0318 Oslo, Norway.
    Porck, Henk
    Paper Hist Collect, Narcisstr 32, NL-2252 XG Voorschoten, Netherlands.
    Kardinaal, Adriaan
    Onderzoeksbur Facto, Leksmondhof 137, NL-1108 ET Amsterdam, Netherlands.
    van Andel, Tinde
    Naturalis Biodivers Ctr, POB 9517, NL-2300 RA Leiden, Netherlands;Leiden Univ, Hist Bot & Gardens, POB 9517, NL-2300 RA Leiden, Netherlands.
    Botanical and floristic composition of the Historical Herbarium of Leonhard Rauwolf collected in the Near East (1573-1575)2018In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 67, no 3, p. 565-580Article in journal (Refereed)
    Abstract [en]

    The German doctor and botanist Leonhard Rauwolf (1535-1596) was the first post-medieval European to travel to the Levant and Mesopotamia. The travel account that he published on his hazardous journey (1573-1575) is well studied, but the plants he collected during his travels have hardly been subjected to scientific study. The fourth volume of Rauwolf's 16th century book herbarium includes plant specimens collected from the area encompassing modern-day Lebanon, Syria and Iraq. We digitized this valuable historic collection, identified all specimens in the herbarium, analyzed its floristic composition, transcribed and translated the Latin and German texts accompanying each specimen and updated the names with the latest accepted nomenclature. The herbarium book includes 191 specimens representing 183 species belonging to 64 families. It includes original specimens of Linnaean type illustrations as well as historical crop cultivars from the Near East. The Rauwolf Herbarium gives a unique insight in the exotic, unknown and useful species of the Near East from the perspective of a 16th century European botanist.

  • 126.
    Ghorbani, Abdolbaset
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Zarre, Shahin
    Gravendeel, Barbara
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Illegal wild collection and international trade of CITES-listed terrestrial orchid tubers in Iran2014In: TRAFFIC Bulletin, ISSN 0267-4297, Vol. 26, no 2, p. 52-58Article in journal (Refereed)
  • 127.
    Gogoi, Rajib
    et al.
    Bot Survey India, Cent Natl Herbarium, PO Bot Garden, Howrah 711103, W Bengal, India.
    Tham, B. B. T.
    Bot Survey India, Arunachal Pradesh Reg Ctr, Itanagar, India.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Borah, Souravjyoti
    Bot Survey India, Arunachal Pradesh Reg Ctr, Itanagar, India.
    Impatiens pseudolaevigata sp. nov. (Balsaminaceae): a new species from Western Arunachal Pradesh, India2017In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 313, no 2, p. 227-230Article in journal (Refereed)
    Abstract [en]

    Impatiens pseudolaevigata from West Kameng district, Arunachal Pradesh, Northeast India, is newly described and illustrated. A detailed description, information on distribution and ecology, and colour photographs are provided for identification of the species. 

  • 128. Gray, Michael A.
    et al.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mayhew, Peter J.
    Hill, Jane K.
    The response of avian feeding guilds to tropical forest disturbance.2007In: Conservation Biology, ISSN 0888-8892, E-ISSN 1523-1739, Vol. 21, no 1, p. 133-141Article in journal (Refereed)
    Abstract [en]

    Anthropogenic habitat disturbance is a major threat to tropical forests and understanding the ecological consequences of this disturbance is crucial for the conservation of biodiversity. There have been many attempts to determine the ecological traits associated with bird species' vulnerability to disturbance, but no attempt has been made to synthesize these studies to show consensus. We analyzed data from 57 published studies (covering 1214 bird species) that investigated the response of tropical bird assemblages to moderate forest disturbance (e.g., selective logging). Our results show that the mean abundance of species from six commonly reported feeding guilds responded differently to disturbance and that species' ecological traits (body size, local population size, and geographic range size) and evolutionary relationships may influence responses in some guilds. Granivore abundance increased significantly and insectivore and frugivore abundance decreased significantly following disturbance. These general conclusions were robust to the effects of ecological traits and phylogeny. Responses of carnivores, nectarivores, and omnivores were less clear, but analyses that accounted for phylogeny indicated that these guilds declined following disturbance. In contrast to the other guilds, the reported responses of carnivores and nectarivores differed among regions (Asia vs. Neotropics) and were influenced by the sampling protocols used in different studies (e.g., time since disturbance), which may explain the difficulty in detecting general responses to disturbance in these guilds. Overall, general patterns governed the responses of species to habitat disturbance, and the differential responses of guilds suggested that disturbance affects trophic organization and thus ecosystem functioning.

  • 129. Hamidi, H. M.
    et al.
    Cardenas, Paco
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Thacker, R. W.
    Diversification and Correlated Trait Evolution in Astrophorid Sponges (Porifera: Demospongiae)2015In: Integrative and Comparative Biology, ISSN 1540-7063, E-ISSN 1557-7023, Vol. 55, no S1, p. E269-E269Article in journal (Other academic)
  • 130. Hareesh, V. S.
    et al.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sabu, M.
    Asteropyrum peltatum (Ranunculaceae): a new generic record for India2016In: Rheedea, ISSN 0971-2313, Vol. 26, no 2, p. 128-130Article in journal (Refereed)
    Abstract [en]

    The genus Asteropyrum J.R. Drumm. & Hutch. (Ranunculaceae) is recorded for the first time for India from Arunachal Pradesh. The species A. peltatum (Franch.) J.R. Drumm. & Hutch. was previously known to occur from southwest China, northern Myanmar and Bhutan. A detailed description along with details on habitat, distribution and photographs is provided here

  • 131.
    Hawksworth, David
    et al.
    Dep de Biologia Vegetal, FAc. de Farmacia, Univ. Complutense, Madrid.
    Santesson, Rolf
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Racoleus, a new genus of sterile filamentous lichen-forming fungi from the tropics, with observations on the nomenclature and typification of Cystocoleus and Racodium2011In: IMA Fungus, ISSN 2210-6340, E-ISSN 2210-6359, Vol. 2, no 1, p. 71-79Article in journal (Refereed)
    Abstract [en]

    Racoleus trichophorus gen. sp.  nov. is described for a ;tropical sterile filamentous lichenized fungus which overgrows various crustose lichens on bark. It shares some features with Cystocoleus and Racodium, but is unique in having non-lichenized arcuate lateral spines. The genus, which is known from China, the Ivory Coast, and Peru, is of uncertain systematic position; on the basis of morphological similarities, however, it may be referred to "? Capnodiales (incertae sedis)" ad interim. In addition, the nomenclature and typification of the monotypic genera Cystocoleus and Racodium are reviewed, and lectotypes selected for the type of each. The available information on the ecology and distribution of these two genera is also summarized, and scanning electron micrographs (SEM) of all three species are presented for the first time.

  • 132.
    He, Ding
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Inferring Ancestry: Mitochondrial Origins and Other Deep Branches in the Eukaryote Tree of Life2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    There are ~12 supergroups of complex-celled organisms (eukaryotes), but relationships among them (including the root) remain elusive. For Paper I, I developed a dataset of 37 eukaryotic proteins of bacterial origin (euBac), representing the conservative protein core of the proto-mitochondrion. This gives a relatively short distance between ingroup (eukaryotes) and outgroup (mitochondrial progenitor), which is important for accurate rooting. The resulting phylogeny reconstructs three eukaryote megagroups and places one, Discoba (Excavata), as sister group to the other two (neozoa). This rejects the reigning “Unikont-Bikont” root and highlights the evolutionary importance of Excavata.

    For Paper II, I developed a 150-gene dataset to test relationships in supergroup SAR (Stramenopila, Alveolata, Rhizaria). Analyses of all 150-genes give different trees with different methods, but also reveal artifactual signal due to extremely long rhizarian branches and illegitimate sequences due to horizontal gene transfer (HGT) or contamination. Removing these artifacts leads to strong consistent support for Rhizaria+Alveolata. This breaks up the core of the chromalveolate hypothesis (Stramenopila+Alveolata), adding support to theories of multiple secondary endosymbiosis of chloroplasts.

    For Paper III, I studied the evolution of cox15, which encodes the essential mitochondrial protein Heme A synthase (HAS). HAS is nuclear encoded (nc-cox15) in all aerobic eukaryotes except Andalucia godoyi (Jakobida, Excavata), which encodes it in mitochondrial DNA (mtDNA) (mt-cox15). Thus the jakobid gene was postulated to represent the ancestral gene, which gave rise to nc-cox15 by endosymbiotic gene transfer. However, our phylogenetic and structure analyses demonstrate an independent origin of mt-cox15, providing the first strong evidence of bacteria to mtDNA HGT.

    Rickettsiales or SAR11 often appear as sister group to modern mitochondria. However these bacteria and mitochondria also have independently evolved AT-rich genomes. For Paper IV, I assembled a dataset of 55 mitochondrial proteins of clear α-proteobacterial origin (including 30 euBacs). Phylogenies from these data support mitochondria+Rickettsiales but disagree on the placement of SAR11. Reducing amino-acid compositional heterogeneity (resulting from AT-bias) stabilizes SAR11 but moves mitochondria to the base of α-proteobacteria. Signal heterogeneity supporting other alternative hypotheses is also detected using real and simulated data. This suggests a complex scenario for the origin of mitochondria.

  • 133.
    He, Ding
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Root of Eukaryote Tree Based on euBac Proteins2011Conference paper (Other academic)
  • 134.
    He, Ding
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Root of Eukaryote Tree Based on euBac Proteins2011Conference paper (Other academic)
    Abstract [en]

    Rooting the eukaryote tree is essential for understanding relationships among the eukaryotic supergroups. A data set was assembled of nuclear-encoded proteins of bacterial origin (euBacs), most of which appear to function primarily in the mitochondrion. Since endosymbiotic transfer of mitochondrial genes to the nucleus occurred after the origin of eukaryotes but before their last common ancestor, this makes bacteria a closer outgroup than Archaea, which have been used in this role previously. A concatenated data set of forty euBacs produces a single strongly supported tree, which places the supergroup Discoba as sister to the remaining mitochondriate eukaryotes. All major competing hypotheses are strongly ruled out with bootstrapping, posterior probabilities and an additive AU test. We have developed a new data set for testing deep eukaryote phylogeny, which strongly resolves all major branches and redefines the position of the root.

  • 135.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fiz-Palacios, Omar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fu, Cheng-Jie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fehling, Johanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tsai, Chun-Chieh
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    An Alternative Root for the Eukaryote Tree of Life2014In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 24, no 4, p. 465-470Article in journal (Refereed)
    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. 

  • 136.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fiz-Palacious, Omar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Root Of Eukaryote Tree Based On euBac Proteins2011Conference paper (Other academic)
  • 137.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fiz-Palacious, Omar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Root of Eukaryote Tree Based on euBac Proteins2011Conference paper (Other academic)
  • 138.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fu, Cheng-Jie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Horizontal transfer of a heme A synthase gene from bactera to jakobid mitochondrial DNAManuscript (preprint) (Other academic)
  • 139.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fu, Cheng-Jie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Multiple Origins of Eukaryotic cox15 Suggest Horizontal Gene Transfer from Bacteria to Jakobid Mitochondrial DNA2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 1, p. 122-133Article in journal (Refereed)
    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.

  • 140.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sierra, Roberto
    University of Geneva.
    Pawlowski, Jan
    University of Geneva.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Reducing long-branch effects in a multi-protein data set identifies a new Rhizaria+Alveolata cladeManuscript (preprint) (Other academic)
  • 141.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sierra, Roberto
    Pawlowski, Jan
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Reducing long-branch effects in multi-protein data uncovers a close relationship between Alveolata and Rhizaria2016In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 101, p. 1-7Article in journal (Refereed)
    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.

  • 142.
    He, Ding
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mining the phylogenetic signal for inferring the origin of mitochondriaManuscript (preprint) (Other academic)
  • 143.
    Hedberg, Inga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Ethiopian Flora Project: the Uppsala perspective2011In: The Ethiopian Flora Project 1980-2009: Exploration, collaboration, inspiration : dedicated to Olov Hedberg / [ed] Inga Hedberg, Eva Persson, Uppsala, 2011, p. 19-25Conference paper (Other academic)
  • 144.
    Hedberg, Inga
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Persson, Eva
    The Ethiopian Flora Project 1980-2009: Exploration, collaboration, inspiration2011Conference proceedings (editor) (Other academic)
  • 145. Hedren, Mikael
    et al.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A replacement name for a species of Hypoestes (Acanthaceae) from Somalia2015In: Willdenowia, ISSN 0511-9618, E-ISSN 1868-6397, Vol. 45, no 1, p. 93-93Article in journal (Refereed)
    Abstract [en]

    Hypoestes canescens Hedren & Thulin, nom. nov., is proposed for the illegitimate name H. cinerea Hedren, non C. B. Clarke.

  • 146.
    Hehenberger, Elisabeth
    et al.
    Univ British Columbia, Dept Bot, Canadian Inst Adv Res, Vancouver, BC, Canada..
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ British Columbia, Dept Bot, Canadian Inst Adv Res, Vancouver, BC, Canada..
    Kolisko, Martin
    Univ British Columbia, Dept Bot, Canadian Inst Adv Res, Vancouver, BC, Canada..
    Keeling, Patrick J.
    Univ British Columbia, Dept Bot, Canadian Inst Adv Res, Vancouver, BC, Canada..
    Functional Relationship between a Dinoflagellate Host and Its Diatom Endosymbiont2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 9, p. 2376-2390Article in journal (Refereed)
    Abstract [en]

    While we know much about the evolutionary patterns of endosymbiotic organelle origins, we know less about how the actual process unfolded within each system. This is partly due to the massive changes endosymbiosis appears to trigger, and partly because most organelles evolved in the distant past. The dinotoms are dinoflagellates with diatom endosymbionts, and they represent a relatively recent but nevertheless obligate endosymbiotic association. We have carried out deep sequencing of both the host and endosymbiont transcriptomes from two dinotoms, Durinskia baltica and Glenodinium foliaceum, to examine how the nucleocytosolic compartments have functionally integrated. This analysis showed little or no functional reduction in either the endosymbiont or host, and no evidence for genetic integration. Rather, host and endosymbiont seem to be bound to each other via metabolites, such as photosynthate exported from the endosymbiont to the host as indicated by the presence of plastidic phosphate translocators in the host transcriptome. The host is able to synthesize starch, using plant-specific starch synthases, as a way to store imported photosynthate.

  • 147.
    Herrmann, Björn
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Isaksson, Jenny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tangrot, Jeanette
    Saleh, Isam
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Versteeg, Bart
    Gravningen, Kirsten
    Bruisten, Sylvia
    Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries2015In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 53, no 7, p. 2172-2179Article in journal (Refereed)
    Abstract [en]

    The Uppsala University Chlamydia trachomatis multilocus sequence type (MLST) database (http://mlstdb.bmc.uu.se) is based on five target regions (non-housekeeping genes) and the ompA gene. Each target has various numbers of alleles-hctB, 89; CT058, 51; CT144, 30; CT172, 38; and pbpB, 35-derived from 13 studies. Our aims were to perform an overall analysis of all C. trachomatis MLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49 ompA gene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 available C. trachomatis whole genomes which were compared to 22 C. trachomatis full genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identified C. trachomatis strains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses.

  • 148.
    Herrmann, Björn
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Stolt, Pelle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Abdeldaim, Guma
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Kirsebom, Leif A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Differentiation and Phylogenetic Relationships in Mycobacterium spp with Special Reference to the RNase P RNA Gene rnpB2014In: Current Microbiology, ISSN 0343-8651, E-ISSN 1432-0991, Vol. 69, no 5, p. 634-639Article in journal (Refereed)
    Abstract [en]

    The rnpB gene encodes for the RNA subunit of the catalytic ribonuclease RNase P and is present in all bacteria and has both conserved and highly variable sequence regions. Determination of rnpB in 35 Mycobacterium spp. showed species specific sequences for all species except the Mycobacterium tuberculosis complex (four species). High sequence variation was seen in the P3, P15 and P19 regions of suggested secondary structures of the corresponding RNase P RNA molecules. Phylogenetic analysis showed that rnpB gave similar tree topologies as 16S rRNA and hsp65 genes. A combined analysis of the three genes increased the number of nodes with significant support from 10 to 19. The results indicate that rnpB is useful for phylogenetic studies and is a possible target for identification and detection of Mycobacterium spp.

  • 149.
    Hiiesalu, Indrek
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    Plant species richness and productivity determine the diversity of soil fungal guilds in temperate coniferous forest and bog habitats2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 18, p. 4846-4858Article in journal (Refereed)
    Abstract [en]

    Fungi have important roles as decomposers, mycorrhizal root symbionts and pathogens in forest ecosystems, but there is limited information about their diversity and composition at the landscape scale. This work aimed to disentangle the factors underlying fungal richness and composition along the landscape-scale moisture, organic matter and productivity gradients. Using high-throughput sequencing, we identified soil fungi from 54 low-productivity Pinus sylvestris-dominated plots across three study areas in Estonia and determined the main predictors of fungal richness based on edaphic, floristic and spatial variables. Fungal richness displayed unimodal relationship with organic matter and deduced soil moisture. Plant richness and productivity constituted the key predictors for taxonomic richness of functional guilds. Composition of fungi and the main ectomycorrhizal fungal lineages and hyphal exploration types was segregated by moisture availability and soil nitrogen. We conclude that plant productivity and diversity determine the richness and proportion of most functional groups of soil fungi in low-productive pine forests on a landscape scale. Adjacent stands of pine forest may differ greatly in the dominance of functional guilds that have marked effects on soil carbon and nitrogen cycling in these forest ecosystems.

  • 150. Hill, M. S.
    et al.
    Hill, A. L.
    Lopez, J.
    Peterson, K. J.
    Pomponi, S.
    Diaz, M. C.
    Thacker, R. W.
    Adamska, M.
    Boury-Esnault, N.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Chaves-Fonnegra, A.
    Danka, E.
    De Laine, B. -O
    Formica, D.
    Hajdu, E.
    Lobo-Hajdu, G.
    Klontz, S.
    Morrow, C. C.
    Patel, J.
    Picton, B.
    Pisani, D.
    Pohlmann, D.
    Redmond, N. E.
    Reed, J.
    Richey, S.
    Riesgo, A.
    Rubin, E.
    Russell, Z.
    Rützler, K.
    Sperling, E. A.
    di Stefano, M.
    Tarver, J. E.
    Collins, A. G.
    Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 1, p. e50437-Article in journal (Refereed)
    Abstract [en]

    Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well-supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.

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