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  • 1.
    Aagaard, Sunniva Margrethe Due
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Reticulate Evolution in Diphasiastrum (Lycopodiaceae)2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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

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

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

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

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

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

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

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

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

    Keyword
    Diphasiastrum, nomenclature, Lycopodium, Lycopodiaceae, typification.
    National Category
    Biological Systematics
    Research subject
    Systematic Botany; Biology with specialization in Systematics
    Identifiers
    urn:nbn:se:uu:diva-99572 (URN)000269774900026 ()
    Available from: 2009-03-16 Created: 2009-03-16 Last updated: 2017-12-13Bibliographically approved
  • 2.
    Aagaard, Sunniva M.D.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Gyllenstrand, Niclas
    Wikström, Niklas
    Homoploid hybridization in Central European Diphasiastrum (Lycopodiaceae).Manuscript (Other academic)
    Abstract [en]

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

  • 3.
    Ahlberg, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Clack, Jennifer
    Luksevics, Ervins
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Zupins, Ivars
    Ventastega curonica and the origin of tetrapod morphology2008In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 453, no 7199, p. 1199-1204Article in journal (Refereed)
    Abstract [en]

    The gap in our understanding of the evolutionary transition from fish to tetrapod is beginning to close thanks to the discovery of new intermediate forms such as Tiktaalik roseae. Here we narrow it further by presenting the skull, exceptionally preserved braincase, shoulder girdle and partial pelvis of Ventastega curonica from the Late Devonian of Latvia, a transitional intermediate form between the 'elpistostegids' Panderichthys and Tiktaalik and the Devonian tetrapods (limbed vertebrates) Acanthostega and Ichthyostega. Ventastega is the most primitive Devonian tetrapod represented by extensive remains, and casts light on a part of the phylogeny otherwise only represented by fragmentary taxa: it illuminates the origin of principal tetrapod structures and the extent of morphological diversity among the transitional forms

  • 4.
    Ajawatanawong, Pravech
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mine the Gaps: Evolution of Eukaryotic Protein Indels and their Application for Testing Deep Phylogeny2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Insertions/deletions (indels) are potentially powerful evolutionary markers, but little is known about their evolution and few tools exist to effectively study them. To address this, I developed SeqFIRE, a tool for automated identification and extraction of indels from protein multiple sequence alignments. The program also extracts conserved alignment blocks, thus covering all major steps in preparing multiple sequence alignments for phylogenetic analysis.

    I then used SeqFIRE to build an indel database, using 299 single copy proteins from a broad taxonomic sampling of mainly multicellular eukaryotes. A total of 4,707 indels were extracted, of which 901 are simple (one genetic event) and 3,806 are complex (multiple events). The most abundant indels are single amino acid simple indels. Indel frequency decreases exponentially with length and shows a linear relationship with host protein size. Singleton indels reveal a strong bias towards insertions (2.31 x deletions on average). These analyses also identify 43 indels marking major clades in Plantae and Fungi (clade defining indels or CDIs), but none for Metazoa.

    In order to study the 3806 complex indels they were first classified by number of states. Analysis of the 2-state complex and simple indels combined (“bi-state indels”) confirms that insertions are over 2.5 times as frequent as deletions. Three-quarters of the complex indels had three-nine states (“slightly complex indels”). A tree-assisted search method was developed allowing me to identify 1,010 potential CDIs supporting all examined major branches of Plantae and Fungi.

    Forty-two proteins were also found to host complex indel CDIs for the deepest branches of Metazoa. After expanding the taxon set for these proteins, I identified a total of 49 non-bilaterian specific CDIs. Parsimony analysis of these indels places Ctenophora as sister taxon to all other Metazoa including Porifera. Six CDIs were also found placing Placozoa as sister to Bilateria. I conclude that slightly complex indels are a rich source of CDIs, and my tree-assisted search strategy could be automated and implemented in the program SeqFIRE to facilitate their discovery. This will have important implications for mining the phylogenomic content of the vast resource of protist genome data soon to become available.

    List of papers
    1. SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
    Open this publication in new window or tab >>SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
    Show others...
    2012 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no W1, p. W340-W347Article in journal (Refereed) Published
    Abstract [en]

    Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

    Keyword
    Indels, Alignment, Conserved blocks
    National Category
    Bioinformatics (Computational Biology) Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-179937 (URN)10.1093/nar/gks561 (DOI)000306670900056 ()
    Available from: 2012-08-27 Created: 2012-08-27 Last updated: 2018-01-12Bibliographically approved
    2. Evolution of protein indels in plants, animals and fungi
    Open this publication in new window or tab >>Evolution of protein indels in plants, animals and fungi
    2013 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 13, p. 140-Article in journal (Refereed) Published
    Abstract [en]

    Background: Insertions/deletions (indels) in protein sequences are useful as drug targets, protein structure predictors, species diagnostics and evolutionary markers. However there is limited understanding of indel evolutionary patterns. We sought to characterize indel patterns focusing first on the major groups of multicellular eukaryotes. Results: Comparisons of complete proteomes from a taxonically broad set of primarily Metazoa, Fungi and Viridiplantae yielded 299 substantial (>250aa) universal, single-copy (in-paralog only) proteins, from which 901 simple (present/absent) and 3,806 complex (multistate) indels were extracted. Simple indels are mostly small (1-7aa) with a most frequent size class of 1aa. However, even these simple looking indels show a surprisingly high level of hidden homoplasy (multiple independent origins). Among the apparently homoplasy-free simple indels, we identify 69 potential clade-defining indels (CDIs) that may warrant closer examination. CDIs show a very uneven taxonomic distribution among Viridiplante (13 CDIs), Fungi (40 CDIs), and Metazoa (0 CDIs). An examination of singleton indels shows an excess of insertions over deletions in nearly all examined taxa. This excess averages 2.31 overall, with a maximum observed value of 7.5 fold. Conclusions: We find considerable potential for identifying taxon-marker indels using an automated pipeline. However, it appears that simple indels in universal proteins are too rare and homoplasy-rich to be used for pure indel-based phylogeny. The excess of insertions over deletions seen in nearly every genome and major group examined maybe useful in defining more realistic gap penalties for sequence alignment. This bias also suggests that insertions in highly conserved proteins experience less purifying selection than do deletions.

    Keyword
    Indels, Rare genomic changes, Phylogeny, Insertion/deletion, Multiple sequence alignment, Eukaryote evolution, Indel profiles
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-204971 (URN)10.1186/1471-2148-13-140 (DOI)000321461800001 ()
    Available from: 2013-08-16 Created: 2013-08-13 Last updated: 2017-12-06Bibliographically approved
    3. An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa
    Open this publication in new window or tab >>An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa
    2014 (English)Article in journal (Refereed) Submitted
    Abstract [en]

    Insertions/deletions (indels) in protein sequences are potential powerful evolutionary markers. However, these characters have rarely been explored systematically at deep phylogenetic levels. Previous analyses of simple (2-state) clade defining indels (CDIs) in universal eukaryotic proteins found none to support any major animal clade. We hypothesized that CDIs might still be found in the remaining population of indels, which we term complex indels. Here, we propose a method for analyzing the simplest class of complex indels the “slightly complex indels”, and use these to investigate deep branches in animal phylogeny. Complex indels with two states, called bi-state indels, show similar evolutionary patterns to singleton simple indels and confirms that insertion mutations are more common than deletions. Exploration of CDIs in 2- to 9-state complex indels shows strong support for all examined branches of fungi and Archaeplastida. Surprisingly, we also found CDIs supporting major branches in animals, particular in vertebrates. We then expanded the search to non-bilaterial animals (Porifera, Cnidaria and Ctenophora). The phylogenetic tree reconstructed by CDIs places the Ctenophore Mnemiopsis leidyi as the deepest branch of animals with 6 CDIs support. Trichoplax adhaerens is closely related to the Bilateria. Moreover, the indel phylogeny shows Nematostella vectensis and Hydra magnipapillata are paraphyletic group and position of Cnidarian branches seems to be problematic in the indel phylogeny because of homoplasy. This might be solved if we discover CDIs from animal specific proteins, which emerged after the universal orthologous proteins.Evolutionary Patterns in Slightly Complex Protein Insertions/Deletions (Indels) and Their Application to the Study of Deep Phylogeny in Metazoa

    National Category
    Other Biological Topics
    Identifiers
    urn:nbn:se:uu:diva-216842 (URN)
    Available from: 2014-01-27 Created: 2014-01-27 Last updated: 2014-04-17Bibliographically approved
  • 5.
    Al Jewari, Caesar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Examining the Root of the Eukaryotic Tree of Life2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Identifying the evolutionary root of eukaryotic tree of life (eToL) is a central problem in systematic biology that has been receiving growing attention. This task has been aided by the development of advanced phylogenetic methods and the availability of large amounts of genomic data from across the tree. Recently, two studies have tried a novel approach to define the eToL root, using euBacteria (instead of the more distantly related Archaea) as the outgroup. The results of these two recent studies are partially overlapping datasets, which produce contradictory results. One study, using mixed eubacterial data (euBac), makes the case for a neozoan-excavate root, while the other study, using alpha-proteobacterial (aP) data, concluded the traditional unikont-bikont root. These two results suggest different theories of early eukaryote evolution. However, there is also evidence of substantial artefacts in these datasets and traces of horizontal gene transfer (HGT), the exchange of DNA between unrelated organisms. This project aims to re-examine the datasets of both publications (61 total protein markers). The work started with updating both datasets with solid new phylogenomic data from the supervisor lab and new publicly available data. I then used these data to systematically investigate the phylogenetic signals of the 61 protein markers across 88 taxa (68 eukaryotes and 20 Bacteria). These were first subjected to preliminary phylogenetic analyses to sort orthologues from paralogues. All orthologues were then combined into a single dataset and subjected to in depth phylogenetic analyses to evaluate the support for various hypotheses. I also investigated potential sources of artefact in the data using traditional and novel methods I devised and developed myself including computer scripts specifically written for this work. I created a pipeline for the data curation process to make it fast and efficient by automating various parts of the workflow, including concatenating the multigene dataset into a super matrix. I estimated the level of incongruence in each dataset, excluded the protein markers that have a strong phylogenetic bias, and reconstructed new datasets. I conclude that the data in hand (protein markers and taxa) contain conflicting and inconsistent phylogenetic signal and that a few proteins can have a very strong effect on the results of the analyses. However, a third possible hypothesis is clearly rejected. This suggests that there are specific artefacts in the data, favouring one or the other of the two remaining hypotheses.

  • 6. Alstrup, Vagn
    et al.
    Grube, Martin
    Motiejunaite, Jurga
    Nordin, Anders
    Uppsala University, Museums etc., Museum of Evolution.
    Zhurbenko, Mikhail
    Lichenicolous fungi from the Skibotn area, Troms, Norway2008In: Graphis Scripta, ISSN 0901-7593, Vol. 20, no 1, p. 1-8Article in journal (Refereed)
    Abstract [en]

    Altogether 93 species of lichenicolous fungi are reported, the majority collected during the Nordic Lichen Society excursion in 2003 to the Skibotn area, Troms, Norway. Cornutispora ciliata, Intralichen cf. lichenum, Opegrapha stereocaulicola and Sphaerulina cf. dubiella are new to Scandinavia, 11 species are new to Norway, and further 42 are new to Troms. Stigmidium aggregata is also reported as new to Greenland. Host lichens, localities, collectors and collection numbers are given.

  • 7.
    Ament-Velásquez, Sandra Lorena
    et al.
    Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universtität München.
    Breedy, Odalisca
    Cortés, Jorge
    Guzman, Hector M.
    Wörheide, Gert
    Vargas, Sergio
    Homoplasious colony morphology and mito-nuclear phylogenetic discordance among Eastern Pacific octocorals2016In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 98, p. 373-381Article in journal (Refereed)
    Abstract [en]

    Octocorals are a diverse and ecologically important group of cnidarians. However, the phylogenetic relationships of many octocoral groups are not well understood and are based mostly on mitochondrial sequence data. In addition, the discovery and description of new gorgonian species displaying unusual or intermediate morphologies and uncertain phylogenetic affinities further complicates the study of octocoral systematics and raises questions about the role played by processes such as plasticity, crypsis, and convergence in the evolution of this group of organisms. Here, we use nuclear (i.e. 28S rDNA) and mitochondrial (mtMutS) markers and a sample of Eastern Pacific gorgonians thought to be remarkable from a morphological point of view to shed light on the morphological diversification among these organisms. Our study reveals the loss of the anastomosed colony morphology in two unrelated lineages of the seafan genusPacifigorgia and offers strong evidence for the independent evolution of a whip-like morphology in two lineages of Eastern Pacific Leptogorgia. Additionally, our data revealed one instance of mito-nuclear discordance in the genera Leptogorgia andEugorgia, which may be the results of incomplete lineage sorting or ancient hybridization–introgression events. Our study stresses the importance of comprehensive taxonomic sampling and the use of independent sources of evidence to address the phylogenetic relationships and clarifying the evolution of octocorals.

  • 8.
    Anderberg, A. A.
    et al.
    Naturhistoriska riksmuseet, Stockholm.
    Ståhl, Bertil
    Gotland University, Department of Biology.
    Källersjö, M.
    Naturhistoriska riksmuseet, Stockholm.
    Maesaceae, a new primuloid family in the order Ericales s.l.2000In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 49, no 2, p. 183-187Article in journal (Refereed)
    Abstract [en]

    Evidence from morphology and molecular sequence data from three chloroplast genes, rbcL, ndhF, and atpB, have shown that the genus Maesa constitutes an evolutionary lineage separate from the other three primuloid families, Theophrastaceae, Myrsinaceae, and Primulaceae. The new family Maesaceae is here formally recognised, its taxonomic status being changed from a subfamily of Myrsinaceae. The new family comprises a single genus, Maesa Forssk., with some 100 species of trees or shrubs; it is diagnosed by characters such as flower pedicels with two bracteoles, a semi-inferior ovary, and indehiscent fruits with many seeds. A key to the major groups of primuloid taxa is presented.

  • 9.
    Anderson, Cajsa Lisa
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Systematisk botanik.
    All we need now is fossils; a new phylogenetic dating method (PATHd8) allowing thousands of taxa and multiple fossil constraints.2006In: Ancient life and modern approaches: Abstracts of the second International Paleontological Congress, 2006, p. 45-Conference paper (Refereed)
    Abstract [en]

    Estimation of divergence times in phylogenetic trees using sequence data

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

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

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

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

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

    necessary.

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

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

    smooth appearance, even if the corresponding phylograms have apparently very

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

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

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

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

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

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

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

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

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

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

  • 10.
    Anderson, Cajsa Lisa
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk botanik.
    Bremer, Kåre
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Friis, Else Marie
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points2005In: American Journal of Botany, Vol. 92, p. 1737-1748Article in journal (Refereed)
    Abstract [en]

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

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

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

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

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

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

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

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

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

    Buxales to 117 my, and Trochodendrales to 116 my.

  • 11.
    Anderson, Cajsa Lisa
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bremer, Kåre
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Friis, Else Marie
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Divergence times of phylogenetically basal eudicots2005In: XVII International Botanical Congress: Vienna, Austria, Europe 17-23 July 2005, 2005, p. 728-Conference paper (Refereed)
    Abstract [en]

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

  • 12.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Eremalche2012In: The Jepson manual: vascular plants of California / [ed] Bruce G. Baldwin, Berkeley: University of California Press , 2012, 2nd ed.Chapter in book (Refereed)
  • 13.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Potential hybridization in real data sets: complex relationships in young flowering plants2007Conference paper (Other academic)
  • 14.
    Andreasen, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldwin, Bruce G.
    Jespon Herbarium, University of California, Berkeley.
    Evolutionary and historical biogeographic perspectives on the genus Arnica (Asteraceae–Madieae): nuclear ribosomal DNA evidence2004Conference paper (Other academic)
  • 15.
    Anslan, Sten
    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.
    Hiiesalu, Indrek
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e234-e240Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable.

  • 16.
    Arup, Ulf
    et al.
    Lund University.
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Fröberg, Lars
    Lund University.
    Frödén, Patrik
    Lund University.
    Knutsson, Tommy
    Lättman, Håkan
    Linköpings universitet.
    Lindblom, Louise
    University of Bergen.
    Mattsson, Jan-Eric
    Södertörns högskola.
    Thell, Arne
    Lund University.
    Westberg, Martin
    Swedish Museum of Natural History.
    Professor Ingvar Kärnefelt - a birthday tribute2009In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 41, p. 453-456Article in journal (Other academic)
  • 17. Arup, Ulf
    et al.
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Grube, Martin
    Mattsson, Jan-Eric
    Wedin, Mats
    The sister group relation of Parmeliaceae2007In: Mycologia, Vol. 99, p. 42-49Article in journal (Refereed)
  • 18.
    Atkinson, Gemma
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms2011In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 28, no 3, p. 1281-1292Article in journal (Refereed)
    Abstract [en]

    Protein synthesis elongation factor G (EF-G) is an essential protein with central roles in both the elongation and ribosome recycling phases of protein synthesis. Although EF-G evolution is predicted to be conservative, recent reports suggest otherwise. We have characterized EF-G in terms of its molecular phylogeny, genomic context and patterns of amino acid substitution. We find that most bacteria carry a single "canonical" EF-G, which is phylogenetically conservative and encoded in an str operon. However, we also find a number of EF-G paralogs. These include a pair of EF-Gs that are mostly found together and in an eclectic subset of bacteria, specifically delta-proteobacteria, spirochaetes and planctomycetes (the "spd" bacteria). These spdEFGs have also given rise to the mitochondrial factors mtEFG1 and mtEFG2, which probably arrived in eukaryotes before the eukaryotic last common ancestor. Meanwhile, chloroplasts apparently use an α-proteobacterial derived EF-G, rather than the expected cyanobacterial form. The long-term co-maintenance of the spd/mtEFGs may be related to their subfunctionalization for translocation and ribosome recycling. Consistent with this, patterns of sequence conservation and site-specific evolutionary rate shifts suggest that the faster evolving spd/mtEFG2 has lost translocation function, but, surprisingly, the protein also shows little conservation of sites related to recycling activity. On the other hand, spd/mtEFG1, although more slowly evolving, shows signs of substantial remodeling. This is particularly extensive in the GTPase domain, including a highly conserved three amino acid insertion in switch I. We suggest that sub-functionalization of the spd/mtEFGs is not a simple case of specialization for subsets of original activities. Rather the duplication allows the release of one paralog from the selective constraints imposed by dual functionality thus allowing it to become more highly specialized. Thus the potential for fine-tuning afforded by subfunctionalization may explain the maintenance of EF-G paralogs.

  • 19. Backlund, Anders
    et al.
    Hunde, Asfaw
    Långström, Elisabeth
    A revision of Cycniopsis (Scrophulariaceae)1993In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 13, p. 185-194Article in journal (Refereed)
  • 20. Barrio-Amorós, César L.
    et al.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The taxonomic status of Rhaebo anderssoni (Melin, 1941)(Anura:Bufonidae)2008In: Salamandra, ISSN 0036-3375, Vol. 44, no 1, p. 59-62Article in journal (Refereed)
  • 21. Becker, N D
    et al.
    Petric, MZgomba, CBoase, CMadoon, MDahl, ChristineUppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Zoology.Kaiser, A
    Mosquitoes and their control2010Collection (editor) (Other academic)
  • 22. Birkebak, Joshua M
    et al.
    Mayor, Jordan R
    Ryberg, Martin
    Department of Ecology and Evolutionary Biology, University of Tennessee.
    Matheny, P Brandon
    A systematic, morphological and ecological overview of the Clavariaceae (Agaricales).2013In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 105, no 4, p. 896-911Article in journal (Refereed)
    Abstract [en]

    The Clavariaceae is a diverse family of mushroom-forming fungi composed of species that produce simple clubs, coralloid, lamellate-stipitate, hydnoid and resupinate sporocarps. Here we present a systematic and ecological overview of the Clavariaceae based on phylogenetic analysis of sequences of the nuclear large subunit ribosomal RNA (nLSU), including nine from type collections. Forty-seven sequences from sporocarps of diverse taxa across the Clavariaceae were merged with 243 environmental sequences from GenBank and analyzed phylogenetically to determine major clades within the family. Four major clades or lineages were recovered: (i) Mucronella, (ii) Ramariopsis-Clavulinopsis, (iii) Hyphodontiella and (iv) Clavaria-Camarophyllopsis-Clavicorona. Clavaria is paraphyletic, within which the lamellate and pileate-stipitate genus Camarophyllopsis is derived and composed of two independent lineages. The monotypic genus Clavicorona also appears nested within Clavaria. The monophyly of Clavaria and Camarophyllopsis, however, cannot be statistically rejected. We compared differing classification schemes for the genera Ramariopsis and Clavulinopsis, most of which are inconsistent with the molecular phylogeny and are statistically rejected. Scytinopogon, a genus classified in the Clavariaceae by several authors, shares phylogenetic affinities with the Trechisporales. Overall 126 molecular operational taxonomic units can be recognized in the Clavariaceae, roughly half of which are known only from environmental sequences, an estimate that exceeds the known number of species in the family. Stable isotope ratios of carbon and nitrogen were measured from specimens representing most major phylogenetic lineages to predict trophic strategies. These results suggest that most non-lignicolous species feature a biotrophic mode of nutrition. Ancestral state reconstruction analysis highlights the taxonomic significance of at least nine morphological traits at various depths in the family tree.

  • 23. Bosak, Sunčica
    et al.
    Šupraha, Luka
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Nanjappa, Deepak
    Kooistra, Wiebe H.C.F.
    Sarno, Diana
    Morphology and phylogeny of four species from the genus Bacteriastrum (Bacillariophyta)2015In: Phycologia, Vol. 54, no 2, p. 130-148Article in journal (Refereed)
  • 24.
    Bremer, Kåre
    et al.
    Uppsala University.
    Chase, Mark W.
    Stevens, Peter F.
    Anderberg, Arne A.
    Backlund, Anders
    Uppsala University.
    Bremer, Birgitta
    Uppsala University.
    Briggs, B. G.
    Endress, Peter K.
    Fay, Michael F.
    Goldblatt, Peter
    Gustafsson, Mat H. G.
    Uppsala University.
    Hoot, S. B.
    Judd, Walter S.
    Kallersjö, Mari
    Kellogg, Elizabeth A.
    Kron, Kathleen A.
    Les, D. H.
    Morton, C. M.
    Nickrent, Daniel L.
    Olmstead, Richard G.
    Price, RA
    Quinn, C. J.
    Rodman, J. E.
    An ordinal classification for the families of flowering plants1998In: ANNALS OF THE MISSOURI BOTANICAL GARDEN, ISSN 0026-6493, Vol. 85, no 4, p. 531-553Article in journal (Other academic)
    Abstract [en]

    Recent cladistic analyses are revealing the phylogeny of flowering plants in increasing detail, and there is support for the monophyly of many major groups above the family level. With many elements of the major branching sequence of phylogeny established

  • 25. Bungartz, Frank
    et al.
    Nordin, Anders
    Uppsala University, Museums etc., Museum of Evolution.
    Grube, Ulrike
    Buellia2008In: Lichen Flora of the Greater Sonoran Desert Region, vol. 3., Arizona State University, Tempe: Lichens Unlimited , 2008, p. 113-179Chapter in book (Other academic)
  • 26. Carr, M.
    et al.
    Leadbeater, B. S. C.
    Hassan, R.
    Nelson, M.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Molecular phylogeny of choanoflagellates, the sister group to Metazoa2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 43, p. 16641-16646Article in journal (Refereed)
    Abstract [en]

    Choanoflagellates are single-celled aquatic flagellates with a unique morphology consisting of a cell with a single flagellum surrounded by a "collar" of microvilli. They have long interested evolutionary biologists because of their striking resemblance to the collared cells (choanocytes) of sponges. Molecular phylogeny has confirmed a close relationship between choanoflagellates and Metazoa, and the first choanoflagellate genome sequence has recently been published. However, molecular phylogenetic studies within choanoflagellates are still extremely limited. Thus, little is known about choanoflagellate evolution or the exact nature of the relationship between choanoflagellates and Metazoa. We have sequenced four genes from a broad sampling of the morphological diversity of choanoflagellates including most species currently available in culture. Phylogenetic analyses of these sequences, alone and in combination, reject much of the traditional taxonomy of the group. The molecular data also strongly support choanoflagellate monophyly rejecting proposals that Metazoa were derived from a true choanoflagellate ancestor. Mapping of a complementary matrix of morphological and ecological traits onto the phylogeny allows a reinterpretation of choanoflagellate character evolution and predicts the nature of their last common ancestor.

  • 27.
    Carr, Martin
    et al.
    Department of Biology, University of York.
    Nelson, Michaela
    Department of Biology, University of York.
    Leadbeater, Barry
    School of Biosciences, University of Birmingham.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Three Families of LTR Retrotransposons are Present in the Genome of the Choanoflagellate Monosiga brevicollis2008In: Protist, ISSN 1434-4610, E-ISSN 1618-0941, Vol. 159, no 4, p. 579-590Article in journal (Refereed)
    Abstract [en]

    The choanoflagellates are a ubiquitous group of nanoflagellates and the sister group of Metazoa. Examination of the initial draft version of the first choanoflagellate genome, that of Monosiga brevicollis, reveals the presence of three novel families of long terminal repeat (LTR) retrotransposons and an apparent absence of non-LTR retrotransposons and transposons. One of the newly discovered LTR families falls in the chromovirus clade of the Ty3/gypsy group while the other two families are closely related members of the Ty1/copia group. Examination of EST sequences and nucleotide analyses show that all three families are transcriptionally active and potentially functional within the genome of M. brevicollis.

  • 28.
    Castroviejo-Fisher, Santiago
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Species Limits, and Evolutionary History of Glassfrogs2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Keyword
    Bioacoustics, Centrolenid frogs, Cryptic species, Glassfrogs, Hyalinobatrachium bergeri, Hyalinobatrachium lemur, Hyalinobatrachium munozorum, Hyalinobatrachium pellucidum, mitochondrial DNA, Synonymy, Taxonomy
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-100922 (URN)000267615900002 ()
    Available from: 2009-04-13 Created: 2009-04-13 Last updated: 2017-12-13Bibliographically approved
  • 29.
    Cavender, James C.
    et al.
    Ohio Univ, Dept Environm & Plant Biol, Athens, OH 45701 USA..
    Landolt, John C.
    Shepherd Univ, Dept Biol, Shepherdstown, WV 25443 USA..
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Perrigo, Allison
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Vadell, Eduardo M.
    JF Kennedy Univ, Escuela Farm & Bioquim, Buenos Aires, DF, Argentina..
    Stephenson, Steven L.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA..
    New species of Polysphondylium from Madagascar2016In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 108, no 1, p. 80-109Article in journal (Refereed)
    Abstract [en]

    Two series of samples collected for isolation of dictyostelid cellular slime molds (dictyostelids) in Madagascar yielded a relatively large number of isolates of Polysphondylium. Most of these turned out to be species new to science that show varying degrees of clustering from unclustered to coremiform as well as an ability to migrate. Migratory ability (phototaxis) is a common feature of species assigned to Group 2 of the Polysphondylia and is common in the new species from Madagascar. Another common feature, clustering, appears to be a strategy for keeping fruiting bodies erect for a longer time in a climate that is relatively dry, whereas migratory ability may function seasonally when there is more rainfall. Thirteen species are described herein. Each of these is characterized by a particular set of distinguishing features, and collectively they expand our concept of the genus Polysphondylium.

  • 30.
    Constantinescu, O.
    Uppsala University, Museums etc., Museum of Evolution.
    The fine structure of the sporangium in Pseudoperonospora humuli (Chromista, Oomycota, Peronosporales)2000In: Cryptogamie, Mycologie, ISSN S0181158400001147/FLA, Vol. 21, no 2, p. 93-101Article in journal (Refereed)
    Abstract [en]

    The ultrastructure of the sporangium, particularly the dehiscence apparatus in Pseudoperonospora humuli is similar to the one described in P. cubensis. This similarity is considered an indication of the homogeneity of the genus Pseudoperonospora. The dehiscence apparatus in P humuli is also similar to those occurring in other closely related, and even more

    distant genera of Oomycota. The importance of the poroid condition in distinguishing Pseudoperonospora

    from Peronospora is emphasised. The dehiscence apparatus is considered as the most appropriate term for the structures present in genera of Oomycota having poroid dissemination

    organs.

  • 31.
    Constantinescu, O.
    Uppsala University, Museums etc., Museum of Evolution.
    The genus Chlorospora Spegazzini, an anamorphic fungus2002In: Sydowia, Vol. 54, no 2, p. 137-141Article in journal (Refereed)
    Abstract [en]

    The type specimen of the unispecific genus Chlorospora was examined. This fungus, considered either a member of the Chromista, Peronosporaceae, or of a doubtful systematic position, is shown to be based on the anamorphic fungus Harzia acremonioides.

  • 32.
    Constantinescu, O.
    et al.
    Uppsala University, Museums etc., Museum of Evolution.
    Voglmayr, H.
    Fatehi, J.
    Thines, M.
    Plasmoverna gen nov., and the taxonomy and nomenclature of Plasmopara (Chromista, Peronosporales)2005In: Taxon, Vol. 54, p. 813-821Article in journal (Refereed)
    Abstract [en]

    After a review of the taxonomy and nomenclature of Plasmopara, it is concluded that this genus contains at least two groups of fungi that can be differentiated on both morphological and molecular grounds. In order to avoid numerous nomenclatural changes, the genus Plasmoverna with seven new combinations (Pv. pygmaea, Pv. alpina, Pv. anemones-dichotomae, Pv. anemones-ranunculoides, Pv. fusca, Pv. hellebori, and Pv. isopyrithalictroides) is introduced to accommodate the species parasitic on Ranunculaceae, which have so far often been referred to as Plasmopara pygmaea s.l. The lectotypification of Plasmopara with Pl. pygmaea, which has been accepted by most authors in recent times, is shown to have been superseded by typification with Pl. nivea. To ensure nomenclatural stability, the ambiguous Pl. nivea is neotypified, and Plasmopara is retained in its current use for the bulk of the species.

  • 33.
    Constantinescu, Ovidiu
    Uppsala University, Museums etc., Museum of Evolution.
    A revision of Basidiophora (Chromista, Peronosporales)1998In: Nova Hedwigia, ISSN 0029-5035, Vol. 66, no 1-2, p. 251-265Article in journal (Other scientific)
    Abstract [en]

    The genus Basidiophora (Chromista, Oomycota, Peronosporales) is revised and restricted to one species, B. entospora, with the recently described B. montana as a synonym. Basidiophora kellermanii is transferred to a new genus, Benua. The two species are de

  • 34.
    Constantinescu, Ovidiu
    et al.
    Uppsala University, Museums etc., Museum of Evolution.
    Thines, Marco
    Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt, Germany.
    Plasmopara halstedii is absent from Australia and New Zealand2010In: Polish Botanical Journal, Vol. 55, no 2, p. 293-298Article in journal (Refereed)
    Abstract [en]

    Plasmopara halstedii (Farl.) Berl. & de Toni is among the most important species hampering commercial sunfl owerproduction in many countries. Downy mildew on Arctotheca and Arctotis collected in Australia and New Zealand has been attributedto Plasmopara halstedii, although it has never been reported on sunfl ower in those two countries. Potentially this makesit diffi cult for Australia and New Zealand to claim to be free of sunfl ower downy mildew; this has implications for quarantineand trade. Here we present morphological and molecular analyses of specimens of Plasmopara on Arctotis and Arctotheca collectedin Australia and New Zealand. Our results demonstrate that these plants are not attacked by Plasmopara halstedii but bya new species which we formally describe as Plasmopara majewskii sp. nov. in this study. Consequently, quarantine regulationsfor P. halstedii need to be enforced in order to protect the commercial sunfl ower industry in Australia and New Zealand.

  • 35.
    Corrales, Carolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Population history and subspecies status of black grouseManuscript (preprint) (Other academic)
  • 36.
    Corrales Duque, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Population Genetic Structure of Black Grouse (Tetrao tetrix): From a Large to a Fine Scale Perspective2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Black grouse (Tetrao tetrix) is a bird species with a lek mating system found in the Palearctic boreal taiga. It is assumed that it has a continuous distribution along Scandinavia and Siberia, whereas in Central Europe it has declined during the last decades. The primary objective of this thesis was to obtain a deeper understanding of the history, systematic classification and the genetic structure of black grouse on different geographical scales using microsatellites and control region mtDNA sequences (CR). I determined how much the mating system, habitat fragmentation and historical population processes have influenced the partitioning of genetic diversity in this species. Phylogeographical results are consistent with a demographic population expansion, and the patterns of postglacial dispersal suggest that a glacial refugium was located somewhere in central Asia, and from there black grouse spread out to Europe following the retreat of glacial ice sheets. I suggest that the two European black grouse subspecies, T. t. Tetrix and T. t. britannicus correspond to only one subspecies: T. t. tetrix, and that this lineage has diverged from T.t. viridanus, a subspecies found in Kazakhstan. The British population is significantly divergent from the remaining Eurasian samples for microsatellites but it is not for mtDNA. Therefore, they should regard as a separate Management Unit and not as a subspecies. Furthermore, British black grouse occur in three independent genetic units, corresponding to Wales, northern England/southern Scotland and northern Scotland. There was also genetic structure within Sweden. Habitat fragmentation is the main cause of population genetic structure in southern Swedish black grouse. In contrast, low levels of genetic differentiation and high connectivity were found in northern Sweden due to female-biased dispersal. On a finer geographical scale, I found genetic differences between leks due to a mixture of related and unrelated individuals within leks. However, mean relatedness values hardly differed from zero. Some leks were similar to one another and I interpret this as a result of variation in local reproductive success and philopatry. These factors would cause genetic structuring but this by itself would not reveal that kin selection is operating within black grouse leks.

    List of papers
    1. Population history and subspecies status of black grouse
    Open this publication in new window or tab >>Population history and subspecies status of black grouse
    (English)Manuscript (preprint) (Other academic)
    National Category
    Biological Systematics
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-150115 (URN)
    Available from: 2011-03-25 Created: 2011-03-25 Last updated: 2011-05-05
    2. Genetic structure among black grouse in Britain: implications for designing conservation units
    Open this publication in new window or tab >>Genetic structure among black grouse in Britain: implications for designing conservation units
    Show others...
    2011 (English)In: Animal Conservation, ISSN 1367-9430, E-ISSN 1469-1795, Vol. 14, no 4, p. 400-408Article in journal (Refereed) Published
    Abstract [en]

    Black grouse in Britain have faced contraction of their range and have declined in numbers during the recent decades. As such, the species is a conservation concern in the UK. In order to aid conservation decisions, the terms Evolutionary Significant Unit (ESU) and Management Unit (MU) have been proposed. An ESU is an independently evolving evolutionary lineage defined by being reciprocally monophyletic for mitochondrial alleles, and which is significantly different from other lineages with regard to nuclear alleles, whereas an MU is operationally defined by only the latter criterion. Using mitochondrial sequences and nuclear microsatellite loci, we failed to find evidence that British black grouse is an ESU. However, British black grouse are sufficiently different from continental black grouse both with respect to mitochondrial and nuclear data to regard them as a separate MU. Furthermore, we present genetic data which suggest that British black grouse presently occur in what are probably three demographically independent units (roughly corresponding to Wales, northern England/southern Scotland and northern Scotland), which are genetically differentiated. The two southern units (Wales and northern England/southern Scotland) have lower genetic diversity and show signs of having lost genetic variability

    Keyword
    Management Unit, Evolutionary Significant Unit, population structure
    National Category
    Biological Systematics Biological Sciences
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-150110 (URN)10.1111/j.1469-1795.2011.00436.x (DOI)000293173900013 ()
    Available from: 2011-03-25 Created: 2011-03-25 Last updated: 2017-12-11Bibliographically approved
    3. Genetic structure of black grouse in Sweden: consequence of historic or contemporary patterns
    Open this publication in new window or tab >>Genetic structure of black grouse in Sweden: consequence of historic or contemporary patterns
    (English)Manuscript (preprint) (Other academic)
    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-150116 (URN)
    Available from: 2011-03-25 Created: 2011-03-25 Last updated: 2011-05-05
    4. Maintenance of gene flow by female-biased dispersal of black grouse, Tetrao tetrix in northern Sweden
    Open this publication in new window or tab >>Maintenance of gene flow by female-biased dispersal of black grouse, Tetrao tetrix in northern Sweden
    2012 (English)In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 153, no 4, p. 1127-1139Article in journal (Refereed) Published
    Abstract [en]

    Sex-biased dispersal is a common phenomenon in most birds. In general, males breed at or near their site of birth while most of the females disperse. We investigated the dispersal patterns and genetic structure of lekking Black Grouse Tetrao tetrix based on ten microsatellite loci. Data for 469 individuals from 25 localities spaced from 45 to 558 km apart revealed low levels of genetic differentiation and high connectivity among studied sites due to female-biased dispersal. The spatial distribution of the genetic variation did not follow an isolation by distance pattern neither for females nor for males. STRUCTURE identified three clusters of male individuals but without any geographical pattern. Only one cluster was identified for females. Several tests of sex-biased dispersal were executed. Most of them showed no difference between sexes, but the mean assignment index and F IS showed a statistically significant female-biased dispersal. Therefore, we consider that the northern Swedish Black Grouse population is a panmictic population. The amount of gene flow throughout time has been consistent with dispersal and with no strong effect of forest fragmentation in the region.

    Abstract [de]

    Geschlechterunterschiede bei der Auswanderung aus dem Heimatterritorium und Ausbreitung gibt es bei den meisten Vogelarten. Üblicherweise brüten Männchen in der Nähe ihres Geburtsorts, während Weibchen vermehrt abwandern. Wir untersuchten Muster in der Verbreitung und die genetische Struktur im Lek balzender Birkhühner Tetrao tetrix anhand von zehn Mikrosatelliten-Loci. Daten von 469 Individuen aus 25 Gebieten, die zwischen 45 und 558 km voneinander entfernt lagen, zeigten geringe genetische Differenzierung und hohe Konnektivität zwischen den Gebieten, gewährleistet durch die Ausbreitung der Weibchen. Die räumliche Verteilung der genetischen Variation zeigte keine Isolation durch hohe Entfernungen, weder für Männchen noch für Weibchen. Das Programm STRUCTURE fand drei Cluster für männliche Individuen, die nicht mit geographischen Mustern übereinstimmten. Bei Weibchen konnte nur ein Cluster identifiziert werden. Wir führten verschiedene Tests für geschlechtsabhängige Verbreitung durch. Die meisten fanden keinen Unterschied zwischen den Geschlechtern, aber der ‘mean assignment index’ und FIS zeigten signifikant stärkere Ausbreitung der Weibchen. Daraus schließen wir, dass die nordschwedische Birkhuhn Population panmiktisch ist. Der genetische Austausch der Populationen konnte stets durch Verteilung weiblicher Individuen erklärt werden, während die Fragmentierung der Wälder in der Region keinen großen Einfluss gehabt zu haben scheint.

    Keyword
    microsatellites, sex-biased dispersal, philopatry
    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-150111 (URN)10.1007/s10336-012-0844-0 (DOI)000308823100013 ()
    Available from: 2011-03-25 Created: 2011-03-25 Last updated: 2017-12-11Bibliographically approved
    5. Fine scale genetic structure in the lek-breeding black grouse Tetrao tetrix
    Open this publication in new window or tab >>Fine scale genetic structure in the lek-breeding black grouse Tetrao tetrix
    (English)Article in journal (Refereed) Submitted
    National Category
    Biological Sciences
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-150113 (URN)
    Available from: 2011-03-25 Created: 2011-03-25 Last updated: 2011-05-18Bibliographically approved
  • 37. Cunnington, James,H.
    et al.
    Constantinescu, Ovidiu
    Uppsala University, Museums etc., Museum of Evolution.
    Basidiophora entospora in Australia2006In: Australasian Mycologist, Vol. 25, no 2, p. 58-60Article in journal (Refereed)
  • 38.
    Cárdenas, Paco
    et al.
    Département Milieux et Peuplements Aquatiques, Muséum National d'Histoire Naturelle.
    Pérez, Thierry
    Université d’Aix-Marseille, Station Marine d’Endoume, Marseille, France.
    Boury-Esnault, Nicole
    Universite´ d’Aix-Marseille, Station Marine d’Endoume, Marseille, France.
    Sponge Systematics Facing New Challenges2012In: Advances in Marine Biology, ISSN 0065-2881, E-ISSN 2162-5875, Vol. 61, p. 79-209Article, review/survey (Refereed)
    Abstract [en]

    Systematics is nowadays facing new challenges with the introduction of newconcepts and new techniques. Compared to most other phyla, phylogenetic relationships among sponges are still largely unresolved. In the past 10 years,the classical taxonomy has been completely overturned and a review of thestate of the art appears necessary. The field of taxonomy remains a prominent discipline of sponge research and studies related to sponge systematics werein greater number in the Eighth World Sponge Conference (Girona, Spain,September 2010) than in any previous world sponge conferences. To understand the state of this rapidly growing field, this chapter proposes to review studies, mainly from the past decade, in sponge taxonomy, nomenclature andphylogeny. In a first part, we analyse the reasons of the current success of this field. In a second part, we establish the current sponge systematics theoretical framework,with the use of (1) cladistics, (2) different codes of nomenclature (Phylo-Code vs. Linnaean system) and (3) integrative taxonomy. Sponges are infamous for their lack of characters. However, by listing and discussing in a third part all characters available to taxonomists, we show how diverse characters are and that new ones are being used and tested, while old ones should be revisited.We then review the systematics of the four main classes of sponges (Hexactinellida, Calcispongiae, Homoscleromorpha and Demospongiae), each time focusing on current issues and case studies. We present a review of the taxonomic changes since the publication of the Systema Porifera (2002), and point to problems a sponge taxonomist is still faced with nowadays. To conclude,we make a series of proposals for the future of sponge systematics. In the light of recent studies, we establish a series of taxonomic changes that the sponge community may be ready to accept. We also propose a series of sponge new names and definitions following the PhyloCode. The issue of phantom species (potential new species revealed by molecular studies) is raised, and we show how they could be dealt with. Finally, we present a general strategy to help us succeed in building a Porifera tree along with the corresponding revised Porifera classification.

  • 39.
    Cárdenas, Paco
    et al.
    Univ Bergen, Dept Biol, N-5020 Bergen, Norway.; Museum Natl Hist Nat, Dept Milieux & Peuplements Aquat, UMR BOREA 7208, F-75005 Paris, France.
    Rapp, Hans Tore
    Univ Bergen, Dept Biol, N-5020 Bergen, Norway.; Univ Bergen, Ctr Geobiol, N-5007 Bergen, Norway.; Uni Environm, N-5006 Bergen, Norway.;.
    A review of Norwegian streptaster-bearing Astrophorida (Porifera: Demospongiae: Tetractinellida), new records and a new species2012In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, no 3253, p. 1-53Article in journal (Refereed)
    Abstract [en]

    We report and describe new material of streptaster-bearing Astrophorida sponges collected in Norway: Characella pachastrelloides, Pachastrella nodulosa sp. nov., Poecillastra compressa, Vulcanella cf. aberrans, Thenea abyssorum,Thenea levis, Thenea muricata and Thenea valdiviae. Because many of these species were described in the end of the 19th century their original descriptions are often incomplete. The Norwegian specimens are the basis for a revision of the morphology, taxonomy and distribution of these species. These are the first records of C. pachastrelloides and V. cf. aberrans from the Norwegian coast. Pachastrella nodulosa sp. nov. differs from Pachastrella monilifera by (i) its knobby surface and (ii) the absence of large oxeas, (iii) its amphiasters have on average less actines and are less spiny, finally (iv) microxeas are rare and with a distinct morphology (although there is some doubt concerning their origin). In the present study, Characella tuberosa (from South Africa), Pachastrella abyssi (from the North-West Atlantic) and Thenea schmidti (from the North-East Atlantic) are resurrected. To help their future identifications, all the Norwegian species described were associated with DNA barcodes: a cytochrome c oxidase subunit I (COI) gene partial fragment and/or a 28S ribosomal gene partial fragment (C1–D2 domains). Furthermore, a key to the streptaster-bearing Astrophorida of the North-East Atlantic and the Mediterranean Sea is also given (lithistids not included).

  • 40.
    Dahl, Christine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology.
    Krzeminska, E
    Designation and description of lectotype Trichocera (Saltrichocera) borealis Lackschewitz 1934. Diptera, Trichoceridae.2008In: Norwegian Journal of Entomology, ISSN 1501-8415, E-ISSN 1894-0692, Vol. 55, no 2Article in journal (Refereed)
  • 41.
    Davis, Robert B
    et al.
    Department of Biology, University of York.
    Baladuf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mayhew, Peter J
    Department of Biology, University of York.
    The origins of species richness in the Hymenoptera: insights from a family-level supertree2010In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 10, article id 109Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The order Hymenoptera (bees, ants, wasps, sawflies) contains about eight percent of all described species, but no analytical studies have addressed the origins of this richness at family-level or above. To investigate which major subtaxa experienced significant shifts in diversification, we assembled a family-level phylogeny of the Hymenoptera using supertree methods. We used sister-group species-richness comparisons to infer the phylogenetic position of shifts in diversification.

    RESULTS: The supertrees most supported by the underlying input trees are produced using matrix representation with compatibility (MRC) (from an all-in and a compartmentalised analysis). Whilst relationships at the tips of the tree tend to be well supported, those along the backbone of the tree (e.g. between Parasitica superfamilies) are generally not. Ten significant shifts in diversification (six positive and four negative) are found common to both MRC supertrees. The Apocrita (wasps, ants, bees) experienced a positive shift at their origin accounting for approximately 4,000 species. Within Apocrita other positive shifts include the Vespoidea (vespoid wasps/ants containing 24,000 spp.), Anthophila + Sphecidae (bees/thread-waisted wasps; 22,000 spp.), Bethylidae + Chrysididae (bethylid/cuckoo wasps; 5,200 spp.), Dryinidae (dryinid wasps; 1,100 spp.), and Proctotrupidae (proctotrupid wasps; 310 spp.). Four relatively species-poor families (Stenotritidae, Anaxyelidae, Blasticotomidae, Xyelidae) have undergone negative shifts. There are some two-way shifts in diversification where sister taxa have undergone shifts in opposite directions.

    CONCLUSIONS: Our results suggest that numerous phylogenetically distinctive radiations contribute to the richness of large clades. They also suggest that evolutionary events restricting the subsequent richness of large clades are common. Problematic phylogenetic issues in the Hymenoptera are identified, relating especially to superfamily validity (e.g. "Proctotrupoidea", "Mymarommatoidea"), and deeper apocritan relationships. Our results should stimulate new functional studies on the causes of the diversification shifts we have identified. Possible drivers highlighted for specific adaptive radiations include key anatomical innovations, the exploitation of rich host groups, and associations with angiosperms. Low richness may have evolved as a result of geographical isolation, specialised ecological niches, and habitat loss or competition.

  • 42.
    Davis, Robert B
    et al.
    Department of Biology, University of York.
    Baldauf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mayhew, Peter J
    Department of Biology, University of York.
    Many hexapod groups originated earlier and withstood extinction events better than previously realized: inferences from supertrees2010In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 277, no 1687, p. 1597-1606Article in journal (Refereed)
    Abstract [en]

    Comprising over half of all described species, the hexapods are central to understanding the evolution of global biodiversity. Direct fossil evidence suggests that new hexapod orders continued to originate from the Jurassic onwards, and diversity is presently higher than ever. Previous studies also suggest that several shifts in net diversification rate have occurred at higher taxonomic levels. However, their inferred timing is phylogeny dependent. We re-examine these issues using the supertree approach to provide, to our knowledge, the first composite estimates of hexapod order-level phylogeny. The Purvis matrix representation with parsimony method provides the most optimal supertree, but alternative methods are considered. Inferring ghost ranges shows richness of terminal lineages in the order-level phylogeny to peak just before the end-Permian extinction, rather than the present day, indicating that at least 11 more lineages survived this extinction than implied by fossils alone. The major upshift in diversification is associated with the origin of wings/wing folding and for the first time, to our knowledge, significant downshifts are shown associated with the origin of species-poor taxa (e.g. Neuropterida, Zoraptera). Polyneopteran phylogeny, especially the position of Zoraptera, remains important resolve because this influences findings regarding shifts in diversification. Our study shows how combining fossil with phylogenetic information can improve macroevolutionary inferences.

  • 43.
    Davis, Robert
    et al.
    Department of Biology, University of York.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Mayhew, Peter
    University of York, Department of Biology.
    Eusociality and the success of the termites: insights from a supertree of dictyopteran families.2009In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 22, no 8, p. 1750-1761Article in journal (Refereed)
    Abstract [en]

    Sociality in insects may negatively impact on species richness. We tested whether termites have experienced shifts in diversification rates through time. Supertree methods were used to synthesize family-level relationships within termites, cockroaches and mantids. A deep positive shift in diversification rate is found within termites, but not in the cockroaches from which they evolved. The shift is responsible for most of their extant species richness suggesting that eusociality is not necessarily detrimental to species richness, and may sometimes have a positive effect. Mechanistic studies of speciation and extinction in eusocial insects are advocated.

  • 44.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kool, Anneleen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Ethnobotanical research and teaching: A Case in Bulgaria2006In: Program of the Society for Economic Botany 47th Annual Meeting, 2006Conference paper (Other (popular science, discussion, etc.))
    Abstract [en]

    Introduction

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

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

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

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

    Objectives

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

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

    of medicinally used plants.

    Methods

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

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

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

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

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

    collect herbarium vouchers.

    Results

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

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

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

    Conclusion

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

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

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

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

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

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

    of a course training ethnobotany students.

  • 45.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Nat Biodivers Ctr, Leiden, Netherlands; Univ Oslo, Nat Hist Museum, Oslo, Norway.
    Ouarghidi, Abderrahim
    Cadi Ayyad Univ, Fac Sci Semlalia, Marrakech, Morocco; Global Div Fdn, Marrakech, Morocco.
    Martin, Gary
    Cadi Ayyad Univ, Fac Sci Semlalia, Marrakech, Morocco; Global Div Fdn, Marrakech, Morocco.
    Abbad, Abdelaziz
    Cadi Ayyad Univ, Fac Sci Semlalia, Marrakech, Morocco; Global Div Fdn, Marrakech, Morocco.
    Kool, Anneleen
    Univ Oslo, Nat Hist Museum, Oslo, Norway.
    DNA Barcoding Reveals Limited Accuracy of Identifications Based on Folk Taxonomy2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 1, article id e84291Article in journal (Refereed)
    Abstract [en]

    Background:

    The trade of plant roots as traditional medicine is an important source of income for many people around theworld. Destructive harvesting practices threaten the existence of some plant species. Harvesters of medicinal roots identifythe collected species according to their own folk taxonomies, but once the dried or powdered roots enter the chain ofcommercialization, accurate identification becomes more challenging.

    Methodology:

    A survey of morphological diversity among four root products traded in the medina of Marrakech wasconducted. Fifty-one root samples were selected for molecular identification using DNA barcoding using three markers,trnH-psbA, rpoC1, and ITS. Sequences were searched using BLAST against a tailored reference database of Moroccanmedicinal plants and their closest relatives submitted to NCBI GenBank.Principal Findings: Combining psbA-trnH, rpoC1, and ITS allowed the majority of the market samples to be identified tospecies level. Few of the species level barcoding identifications matched the scientific names given in the literature,including the most authoritative and widely cited pharmacopeia.

    Conclusions/Significance:

    The four root complexes selected from the medicinal plant products traded in Marrakech allcomprise more than one species, but not those previously asserted. The findings have major implications for the monitoringof trade in endangered plant species as morphology-based species identifications alone may not be accurate. As a result,trade in certain species may be overestimated, whereas the commercialization of other species may not be recorded at all.

  • 46.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Schaefer, Hanno
    Harvard University, Department of Organismic and Evolutionary Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Renner, Susanne S.
    University of Munich (LMU), Systematic Botany and Mycology.
    Evolution and loss of long-fringed petals: A case study using a dated phylogeny of the snake gourds, Trichosanthes (Cucurbitaceae)2012In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 12, p. 108-Article in journal (Refereed)
    Abstract [en]

    Background

    The Cucurbitaceae genus Trichosanthes comprises 90–100 species that occur from India to Japan and southeast to Australia and Fiji. Most species have large white or pale yellow petals with conspicuously fringed margins, the fringes sometimes several cm long. Pollination is usually by hawkmoths. Previous molecular data for a small number of species suggested that a monophyletic Trichosanthes might include the Asian genera Gymnopetalum (four species, lacking long petal fringes) and Hodgsonia (two species with petals fringed). Here we test these groups’ relationships using a species sampling of c. 60% and 4759 nucleotides of nuclear and plastid DNA. To infer the time and direction of the geographic expansion of the Trichosanthes clade we employ molecular clock dating and statistical biogeographic reconstruction, and we also address the gain or loss of petal fringes.

    Results

    Trichosanthes is monophyletic as long as it includes Gymnopetalum, which itself is polyphyletic. The closest relative of Trichosanthes appears to be the sponge gourds, Luffa, while Hodgsonia is more distantly related. Of six morphology-based sections in Trichosanthes with more than one species, three are supported by the molecular results; two new sections appear warranted. Molecular dating and biogeographic analyses suggest an Oligocene origin of Trichosanthes in Eurasia or East Asia, followed by diversification and spread throughout the Malesian biogeographic region and into the Australian continent.

    Conclusions

    Long-fringed corollas evolved independently in Hodgsonia and Trichosanthes, followed by two losses in the latter coincident with shifts to other pollinators but not with long-distance dispersal events. Together with the Caribbean Linnaeosicyos, the Madagascan Ampelosicyos and the tropical African Telfairia, these cucurbit lineages represent an ideal system for more detailed studies of the evolution and function of petal fringes in plant-pollinator mutualisms.

  • 47.
    de Boer, Hugo J.
    et al.
    Avd f systematisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thulin, Mats
    Avd f systematisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Lectotypification of Callicocca ipecacuanha Brot. and neotypification of Cephaelis acuminata H.Karst., with reference to the drug ipecac2005In: Taxon, ISSN 0040-0262, Vol. 54, no 4, p. 1080-1082Article in journal (Refereed)
  • 48. Delgado-Salinas, Alfonso
    et al.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pasquet, Rémy
    Weeden, Norm
    Lavin, Matt
    Vigna (Leguminosae) sensu lato: The names and identities of the American segregate2011In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 98, no 10, p. 1694-1715Article in journal (Refereed)
    Abstract [en]

    Premise of study: The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology.

    Methods: The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives.

    Key results: The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna.

    Conclusions: American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6–7 million yr, which belies much greater floral variation in the Americas.

  • 49.
    den Tex, Robert-Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Patterns and Processes of Evolution in Sundaland2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biodiversity in the tropics is disproportionately high compared to other habitats, and also under disproportionate threat from human impact. It is necessary to understand how this diversity evolved and how it is partitioned across space in order to preserve it. In this thesis I construct phylogenies of tropical forest dependent vertebrates from Southeast Asia and the islands of the Sunda shelf, a region referred to as Sundaland. I focus on the tree squirrels (genus Sundasciurus) and Asian barbets (Aves: Family Megalaimidae), two taxa with similar ecological characteristics. I use these phylogenies to test hypotheses that have been put forward to explain high levels of tropical diversity including the Pleistocene pump and museum hypotheses. I also use phylogenies to elucidate phylogeographic patterns within the region. I find no evidence for an increase in speciation in the Pleistocene, but I do find within species structure that dates to this period. Common phylogeographic patterns were identified between many forest dependent vertebrates that suggest that populations on the island of Sumatra are generally more closely related to Malay Peninsula populations than to populations on Borneo.

    From a methodological viewpoint we propose careful usage of universal primers in ancient DNA studies because of our finding of increased risk of amplifying pseudogenes of the mtDNA.

    List of papers
    1. Biogeography of the Sunda Shelf: a multi species comparison
    Open this publication in new window or tab >>Biogeography of the Sunda Shelf: a multi species comparison
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-152227 (URN)
    Available from: 2011-04-27 Created: 2011-04-27 Last updated: 2011-07-01
    2. Speciation and extinction in the tropics: insights from Asian barbets
    Open this publication in new window or tab >>Speciation and extinction in the tropics: insights from Asian barbets
    (English)Manuscript (preprint) (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-152223 (URN)
    Available from: 2011-04-27 Created: 2011-04-27 Last updated: 2011-07-01
    3. Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus
    Open this publication in new window or tab >>Speciation dynamics in the SE Asian tropics: Putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus
    2010 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 55, no 2, p. 711-720Article in journal (Refereed) Published
    Abstract [en]

    Tropical rainforests are well known for their extraordinarily high levels of biodiversity. The origin of this species richness is still debated. For instance, the museum hypothesis states that over evolutionary time more and more species will accumulate with relatively few extinctions. In contrast, the Pleistocene diversification model argues that during the last 2 million years, climatic factors (glaciations) caused environmental changes that drove isolation and vicariant speciation events. In this study, we construct a molecular phylogeny of the Sundaland (Malay Peninsula, Sumata, Borneo, Palawan) and Greater Mindanao (Mindanao, Samar, Leyte) tree squirrels (genus Sundasciurus). Our results show that most speciation events in this forest dependent taxon occurred before the Pleistocene and that even the timing of intra-specific splits among populations from different landmasses are relatively old. Additionally, we found unexpectedly high divergence within and between highland populations of S. tenuis on Sumatra and the Malay Peninsula, highlighting the importance of Pliocene events in both speciation and within species divergences in this region. (C) 2010 Elsevier Inc. All rights reserved.

    Keyword
    Cytochrome b, Fib6, c-myc, FTH, POR, GBG, HMG1, Sunda shelf, Pleistocene species pump, Molecular dating, RY coding
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-136338 (URN)10.1016/j.ympev.2009.12.023 (DOI)000276875300031 ()
    Available from: 2010-12-13 Created: 2010-12-11 Last updated: 2017-12-11Bibliographically approved
    4. Red and yellow: the phylogeography of the coppersmith barbet (Aves: Megalaima haemacephala)
    Open this publication in new window or tab >>Red and yellow: the phylogeography of the coppersmith barbet (Aves: Megalaima haemacephala)
    (English)Manuscript (preprint) (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-152224 (URN)
    Available from: 2011-04-27 Created: 2011-04-27 Last updated: 2011-07-01
    5. Nuclear copies of mitochondrial genes: another problem for ancient DNA
    Open this publication in new window or tab >>Nuclear copies of mitochondrial genes: another problem for ancient DNA
    2010 (English)In: Genetica, ISSN 0016-6707, E-ISSN 1573-6857, Vol. 138, no 9-10, p. 979-984Article in journal (Refereed) Published
    Abstract [en]

    The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.

    Keyword
    Numt, aDNA, Sundasciurus, Mitochondria, Universal primers
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-134537 (URN)10.1007/s10709-010-9481-9 (DOI)000282432000007 ()
    Available from: 2010-11-30 Created: 2010-11-29 Last updated: 2017-12-12Bibliographically approved
  • 50. Dillman, Karen L.
    et al.
    Ahti, Teuvo
    Bjoerk, Curtis R.
    Clerc, Philippe
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Goward, Trevor
    Hafellner, Josef
    Perez-Ortega, Sergio
    Printzen, Christian
    Savic, Sanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Schultz, Matthias
    Svensson, Mans
    Thor, Goran
    Tonsberg, Tor
    Vitikainen, Orvo
    Westberg, Martin
    Spribille, Toby
    New records, range extensions and nomenclatural innovations for lichens and lichenicolous fungi from Alaska, USA2012In: Herzogia, ISSN 0018-0971, Vol. 25, no 2, p. 177-210Article in journal (Refereed)
    Abstract [en]

    New records, range extensions and nomenclatural innovations for lichens and lichenicolous fungi from Alaska, U.S.A. - Herzogia 25: 177-210. Surveys of lichens and lichenicolous fungi have been taking place in the U.S. state of Alaska for more than 160 years, but until now assessing the full extent of their diversity has been hampered by the lack of a comprehensive and synonymized baseline inventory. In this paper we will begin to redress this by resolving outstanding nomenclatural issues and providing voucher data for a forthcoming catalog of Alaskan lichens, specifically: 1) synonymization,and/or resolution of status of species previously reported from Alaska, with emphasis on Alaskan types; 2) species new to the Alaska lichen biota; and 3) biogeographically significant new records from within Alaska. We report 91 species new to the flora of Alaska, including 65 lichens, three saprophytic calicioid fungi and 23 lichenicolous fungi. Of these, we report thirteen species, Biatora sphaeroidiza, Biatorella conspurcans, Chaenothecopsis arthoniae, Collemopsidium foveolatum, Dactylospora frigida, Halospora discrepans, Lecanora bryopsora, Opegrapha geographicola, Peltigera lyngei, Petractis clausa, Protoblastenia cyclospora, Thelocarpon impressellum and Usnea cylindrica as new to North America. In addition, Arthonia pruinata and Flavocetraria minuscula are new to Canada and Adelococcus alpestris new to the United States. We further place the following five names into synonymy: Lecania disceptans (Nyl.) Lynge [= Halecania alpivaga (Th.Fr.) M.Mayrhofer], Lecidea pallidella Nyl. [= Lecania subfuscula (Nyl.) S.Ekman], Lempholemma triptodes (Nyl.) Zahlbr. Leciophysma finmarkicum Th.Fr.), Polyblastia obtenta (Nyl.) Lynge [= Sporodictyon terrestre (Th.Fr.) S.Savic & Tibell], and Verrucaria pernigrata Nyl. [= Protothelenella sphinctrinoides (Nyl.) H.Mayrhofer & Poelt]. We propose restoring the long overlooked taxon Polyblastia exalbida (Nyl.) Zahlbr., currently known only from Alaska, to the North American lichen checklist. Finally, we propose the new combination Puttea caesia (Fr.) M.Svensson & T.Sprib. to replace Lecidea symmictella Nyl., which becomes a synonym.

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