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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.

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

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

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

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

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

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

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

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

    Keywords
    Diphasiastrum, nomenclature, Lycopodium, Lycopodiaceae, typification.
    National Category
    Biological Systematics
    Research subject
    Systematic Botany; Biology with specialization in Systematics
    Identifiers
    urn:nbn:se:uu:diva-99572 (URN)000269774900026 ()
    Available from: 2009-03-16 Created: 2009-03-16 Last updated: 2017-12-13Bibliographically approved
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  • 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.
    Abarenkov, Kessy
    et al.
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Kristiansson, Erik
    Chalmers Univ Technol, Dept Math Sci, Gothenburg, Sweden.;Univ Gothenburg, Gothenburg, Sweden..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nogal-Prata, Sandra
    Real Jardin Bot CSIC, Dept Mycol, Madrid, Spain..
    Gomez-Martinez, Daniela
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Stueer-Patowsky, Katrin
    Tech Univ Munich, Chair Urban Water Syst Engn, Coulombwall 3, D-85748 Garching, Germany..
    Jansson, Tobias
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Polme, Sergei
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Ghobad-Nejhad, Masoomeh
    Iranian Res Org Sci & Technol, Dept Biotechnol, POB 3353-5111, Tehran 3353136846, Iran..
    Corcoll, Natalia
    Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Scharn, Ruud
    Univ Gothenburg, Dept Earth Sci, Box 460, S-40530 Gothenburg, Sweden..
    Sanchez-Garcia, Marisol
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden..
    Khomich, Maryia
    Univ Bergen, Dept Clin Sci, Box 7804, N-5020 Bergen, Norway..
    Wurzbacher, Christian
    Tech Univ Munich, Chair Urban Water Syst Engn, Coulombwall 3, D-85748 Garching, Germany..
    Nilsson, R. Henrik
    Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    The curse of the uncultured fungus2022In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 86, p. 177-194Article in journal (Refereed)
    Abstract [en]

    The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget lowresolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length that represent truly unidentifiable fungal taxa - and what proportion of them that would have deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.

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    FULLTEXT01
  • 4.
    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

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    FULLTEXT01
  • 5.
    Aignon, Hyppolite L.
    et al.
    Univ Parakou, Res Unit Trop Mycol & Plant Soil Fungi Interact, Fac Agron, 03 BP 125, Parakou, Benin..
    Jabeen, Sana
    Univ Educ, Dept Bot, Div Sci & Technol, Lahore, Pakistan..
    Naseer, Arooj
    Univ Punjab, Dept Bot, Quaid E Azam Campus, Lahore 54590, Pakistan..
    Yorou, Nourou S.
    Univ Parakou, Res Unit Trop Mycol & Plant Soil Fungi Interact, Fac Agron, 03 BP 125, Parakou, Benin..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Three new species of Inosperma (Agaricales, Inocybaceae) from Tropical Africa2021In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 77, p. 97-116Article in journal (Refereed)
    Abstract [en]

    Here, we describe three new species of Inosperma from Tropical Africa: Inosperma africanum, I. bulhomarginatum and I. flavobrunneum. Morphological and molecular data show that these species have not been described before, hence need to be described as new. The phylogenetic placements of these species were inferred, based on molecular evidence from sequences of 28S and RPB2. Additional analysis using ITS dataset shows interspecific variation between each species. Phylogenetic analyses resolve I. flavobrunneum in Old World Tropical lade I with weak support, I. bulbomarginatum is sister of Old World Tropical clack 1 and I. africanum is indicated as sister to the rest of Inosperma. Complete description and illustrations, including photographs and line drawings, are presented for each species. A new combination of Inocybe shawarensis into Inosperma is also proposed.

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    FULLTEXT01
  • 6.
    Aignon, Hyppolite L.
    et al.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Plant Soil Fungi Interact, 03 BP 125, Parakou, Benin..
    Naseer, Arooj
    Univ Punjab, Dept Bot, Quaid E Azam Campus, Lahore 54590, Pakistan..
    Matheny, Brandon P.
    Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN 37996 USA..
    Yorou, Nourou S.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Plant Soil Fungi Interact, 03 BP 125, Parakou, Benin..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mallocybe africana (Inocybaceae, Fungi), the first species of Mallocybe described from Africa2021In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 478, no 1, p. 49-60Article in journal (Refereed)
    Abstract [en]

    The family Inocybaceae has been poorly studied in Africa. Here we describe the first species of the genus Mallocybe from West African and Zambian woodlands dominated by ectomycorrhizal trees of Fabaceae and Phyllanthaceae. The new species M. africana is characterized by orange-brown fruitbodies, a fibrillose pileus, a stipe tapered towards the base and large ellipsoid basidiospores. It resembles many north and south temperate species of Mallocybe but is most closely related to the southeast Asian tropical species, M. errata. M. africana is widely distributed in West Africa (Benin, Togo, Burkina Faso and Ivory Coast) extending to South-eastern Africa in Zambia. Phylogenetic analyses based on 5.8S rDNA, nLSU and RPB2 sequence data confirm that M. africana is nested within Mallocybe. A complete morphological description and illustrations, including photographs and line drawings, are presented.

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  • 7.
    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/.

    Keywords
    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: 2019-08-28Bibliographically 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, 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.

    Keywords
    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: 2024-01-17Bibliographically 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)Manuscript (preprint) (Other academic)
    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: 2024-04-03Bibliographically approved
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  • 8.
    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.

  • 9.
    Al Jewari, Caesar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Resolving deep nodes of eukaryote phylogeny2022Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    My thesis aims to solve deep nodes in the eukaryote tree of life (eToL), by developing new data sets and new approaches to analysing them. In paper I, I described a dataset of 76 universal eukaryotic proteins of bacterial descent (euBacs), in order to test the relations among the three main divisions of mitochondriate eukaryotes (Amorphea, Diaphretickes and Discoba). I developed two protocols to identify problematic data. The conJac protocol analyzes data by jackknifing to detect outlier sequences, while conWin uses a sliding window to find sequence fragments of potentially foreign origin. Phylogenetic analyses of the 76 euBacs, with and without conWin or conJac filtering place Discoba as the sister group to Amorphea and Diaphretickes. The results are largely consistent and highly supported under various evolutionary models except for highly complex CAT models. In paper II, I describe a dataset of 198 universal eukaryote proteins of archaeal ancestry (euArcs), which includes the remaining eukaryotes, informally referred to as amitochondriate excavate. These were excluded from the previous study because they lack euBacs. Phylogenetic analyses of the euArc dataset place the amitochondriate excavate as the first three branches of eToL, followed by Discoba, the only mitochondriate excavates, which appear as a sister group to the remaining eukaryotes. I also developed a protocol using predicted protein structures to increase the fitness of the model without inflating the parameter space, allowing me to conduct a series of control analyses and further support the multi-excavate root. In Paper III, I describe a new application of reciprocal-rooting using concatenated sequences, which I then use to test the euArc root. I also developed two sampling protocols unique to this kind of data. The protocols confirm the multi-excavate euArc root, which indicates that eukaryotes arose from an excavate ancestor. Paper IV describes a follow-up on the ConWin results from Paper I. These show moderate to strong support for mosaicism in 16 euBac proteins from diverse metabolic pathways and donor lineages. In summary, this thesis presents a novel root for the eukaryote tree of life. The new root requires revision of fundamental theories of eukaryote evolution including the source and timing of mitochondrial origins. The methods I have developed are applicable to many different kinds of phylogenetic studies, and the new protein structure model should make these analyses faster, more flexible, and more widely available.

    List of papers
    1. Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models
    Open this publication in new window or tab >>Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models
    2022 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836XArticle in journal (Refereed) Epub ahead of print
    Abstract [en]

    Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees. However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artifacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, whereas ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi, and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in undersampled lineages, whereas ConWin analyses of Discoba, the most undersampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.

    National Category
    Biological Systematics
    Identifiers
    urn:nbn:se:uu:diva-484535 (URN)10.1093/sysbio/syac029 (DOI)000804041500001 ()35412616 (PubMedID)
    Funder
    Swedish Research Council, 2017-04351
    Available from: 2022-09-13 Created: 2022-09-13 Last updated: 2022-10-18
    2. An excavate root for the eukaryote tree of life
    Open this publication in new window or tab >>An excavate root for the eukaryote tree of life
    2023 (English)In: Science Advances, ISSN 2375-2548, Vol. 9, no 17, article id eade4973Article in journal (Other academic) Published
    Abstract [en]

    Much of the higher-order phylogeny of eukaryotes is well resolved, but the root remains elusive. We assembled a dataset of 183 eukaryotic proteins of archaeal ancestry to test this root. The resulting phylogeny identifies four lineages of eukaryotes currently classified as “Excavata” branching separately at the base of the tree. Thus, Parabasalia appear as the first major branch of eukaryotes followed sequentially by Fornicata, Preaxostyla, and Discoba. All four excavate branch points receive full statistical support from analyses with commonly used evolutionary models, a protein structure partition model that we introduce here, and various controls for deep phylogeny artifacts. The absence of aerobic mitochondria in Parabasalia, Fornicata, and Preaxostyla suggests that modern eukaryotes arose under anoxic conditions, probably much earlier than expected, and without the benefit of mitochondrial respiration.

    Place, publisher, year, edition, pages
    American Association for the Advancement of Science (AAAS), 2023
    National Category
    Biological Systematics Ecology Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-484543 (URN)10.1126/sciadv.ade4973 (DOI)000989268500015 ()37115919 (PubMedID)
    Funder
    Swedish Research Council, 2017-04351Swedish Research Council FormasForte, Swedish Research Council for Health, Working Life and Welfare, 2017-04351
    Available from: 2022-09-13 Created: 2022-09-13 Last updated: 2023-10-04Bibliographically approved
    3. Reciprocal rooting with concatenation supports the multi-excavate root
    Open this publication in new window or tab >>Reciprocal rooting with concatenation supports the multi-excavate root
    (English)Manuscript (preprint) (Other academic)
    National Category
    Biological Systematics
    Research subject
    Biology with specialization in Systematics
    Identifiers
    urn:nbn:se:uu:diva-484545 (URN)
    Available from: 2022-09-13 Created: 2022-09-13 Last updated: 2022-09-13
    4. Widespread mosaicism in eukaryotic genes of bacterial ancestry
    Open this publication in new window or tab >>Widespread mosaicism in eukaryotic genes of bacterial ancestry
    (English)Manuscript (preprint) (Other academic)
    National Category
    Biological Systematics
    Research subject
    Biology with specialization in Systematics
    Identifiers
    urn:nbn:se:uu:diva-484571 (URN)
    Funder
    Swedish Research Council, 2017-04351
    Available from: 2022-09-13 Created: 2022-09-13 Last updated: 2022-09-13
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  • 10.
    Al Jewari, Caesar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    An excavate root for the eukaryote tree of life2023In: Science Advances, ISSN 2375-2548, Vol. 9, no 17, article id eade4973Article in journal (Other academic)
    Abstract [en]

    Much of the higher-order phylogeny of eukaryotes is well resolved, but the root remains elusive. We assembled a dataset of 183 eukaryotic proteins of archaeal ancestry to test this root. The resulting phylogeny identifies four lineages of eukaryotes currently classified as “Excavata” branching separately at the base of the tree. Thus, Parabasalia appear as the first major branch of eukaryotes followed sequentially by Fornicata, Preaxostyla, and Discoba. All four excavate branch points receive full statistical support from analyses with commonly used evolutionary models, a protein structure partition model that we introduce here, and various controls for deep phylogeny artifacts. The absence of aerobic mitochondria in Parabasalia, Fornicata, and Preaxostyla suggests that modern eukaryotes arose under anoxic conditions, probably much earlier than expected, and without the benefit of mitochondrial respiration.

    Download full text (pdf)
    fulltext
  • 11.
    Al Jewari, Caesar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Conflict over the Eukaryote Root Resides in Strong Outliers, Mosaics and Missing Data Sensitivity of Site-Specific (CAT) Mixture Models2022In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836XArticle in journal (Refereed)
    Abstract [en]

    Phylogenetic reconstruction using concatenated loci ("phylogenomics" or "supermatrix phylogeny") is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees. However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artifacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from a central mean for each individual sequence, whereas ConWin uses a sliding window to screen for incongruent protein fragments (mosaics). Both methods allow selective masking of individual sequences or sequence fragments in order to minimize missing data, an important consideration for resolving deep splits with limited data. Analyses focused on a set of 76 eukaryotic proteins of bacterial ancestry previously used in various combinations to assess the branching order among the three major divisions of eukaryotes: Amorphea (mainly animals, fungi, and Amoebozoa), Diaphoretickes (most other well-known eukaryotes and nearly all algae) and Excavata, represented here by Discoba (Jakobida, Heterolobosea, and Euglenozoa). ConJak analyses found strong outliers to be concentrated in undersampled lineages, whereas ConWin analyses of Discoba, the most undersampled of the major lineages, detected potentially incongruent fragments scattered throughout. Phylogenetic analyses of the full data using an LG-gamma model support a Discoba sister scenario (neozoan-excavate root), which rises to 99-100% bootstrap support with data masked according to either protocol. However, analyses with two site-specific (CAT) mixture models yielded widely inconsistent results and a striking sensitivity to missing data. The neozoan-excavate root places Amorphea and Diaphoretickes as more closely related to each other than either is to Discoba, a fundamental relationship that should remain unaffected by additional taxa.

  • 12.
    Al Jewari, Caesar
    et al.
    Department of Organismal Biology, Uppsala University Program in Systematic Biology, , Uppsala 75236, Sweden.
    Baldauf, Sandra L
    Department of Organismal Biology, Uppsala University Program in Systematic Biology, , Uppsala 75236, Sweden.
    Reciprocal rooting with concatenation supports the multi-excavate rootManuscript (preprint) (Other academic)
  • 13. 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.

  • 14. Alström, Per
    et al.
    Cibois, Alice
    Fjeldså, Jon
    Fuchs, Jerome
    The worldwide expansion of ‘higher’ passerines, and some ancient, relictual lineages2020In: The Largest Avian Radiation: The Evolution of Perching Birds, or the Order Passeriformes / [ed] Fjeldså, J., Christidis, L., Ericson, P.G.P., Barcelona: Lynx Edicions , 2020Chapter in book (Other academic)
  • 15.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    de Juana, Eduardo
    Donald, Paul F.
    Suárez, Francisco
    Mediterranean Short-toed Lark (Alaudala rufescens)2023Other (Other academic)
  • 16.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Donald, Paul F.
    Sharpe's Lark (Mirafra sharpii)2022Other (Other academic)
  • 17.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Donald, Paul F.
    Turkestan Short-toed Lark (Alaudala heinei)2023Other (Other academic)
  • 18.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 , China.
    Mohammadi, Zeinolabedin
    Donald, Paul F
    Nymark, Marianne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Enbody, Erik D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Department of Biomolecular Engineering, University of California, Santa Cruz , Santa Cruz, CA 95060 , USA.
    Irestedt, Martin
    Elisha, Emmanuel Barde
    Ndithia, Henry K
    Tieleman, B Irene
    Engelbrecht, Derek
    Olsson, Urban
    Rancilhac, Loïs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Stervander, Martin
    Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)2023In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642Article in journal (Refereed)
    Abstract [en]

    The species complex comprising the rufous-naped lark Corypha africana, Sharpe’s lark Corypha sharpii, the red-winged lark Corypha hypermetra, the Somali long-billed lark Corypha somalica and Ash’s lark Corypha ashi encompasses 31 recognised taxa across sub-Saharan Africa, many of which are extremely poorly known and some not observed for decades. Only 17 taxa have been studied molecularly and none comprehensively for morphology, vocalisations or other behaviours. Here, we undertake comprehensive integrative taxonomic analyses based on plumage and morphometrics (for 97% of the taxa), mitochondrial and nuclear loci (77%), ≤ 1.3 million genome-wide single nucleotide polymorphisms (68%), song (many described for the first time; 52%) and additional behavioural data (45%). All polytypic species as presently circumscribed are paraphyletic, with eight primary clades separated by ≤ 6.3–6.8 Myr, broadly supported by plumage, morphometrics, song and other behaviours. The most recent divergences concern sympatric taxon pairs usually treated as separate species, whereas the divergence of all clades including C. africana subspecies is as old as sister species pairs in other lark genera. We propose the recognition of nine instead of five species, while C. ashi is synonymised with C. somalica rochei as C. s. ashi. The geographical distributions are incompletely known, and although the nine species are generally para-/allopatric, some might be sympatric.

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    fulltext
  • 19.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
    Mohammadi, Zeinolabedin
    Enbody, Erik D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Department of Biomolecular Engineering, University of California, Santa Cruz, 95060, Santa Cruz, CA, USA.
    Irestedt, Martin
    Engelbrecht, Derek
    Crochet, Pierre-André
    Guillaumet, Alban
    Rancilhac, Loïs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Tieleman, B. Irene
    Olsson, Urban
    Donald, Paul F.
    Stervander, Martin
    Systematics of the avian family Alaudidae using multilocus and genomic data2023In: Avian Research, E-ISSN 2053-7166, Vol. 14, article id 100095Article in journal (Refereed)
    Abstract [en]

    The family Alaudidae, larks, comprises 93–100 species (depending on taxonomy) that are widely distributed across Africa and Eurasia, with single species extending their ranges to North and northernmost South America and Australia. A decade-old molecular phylogeny, comprising ∼80% of the species, revealed multiple cases of parallel evolution and large variation in rates of morphological evolution, which had misled taxonomists into creating many non-monophyletic genera. Here, we reconstruct the phylogeny of the larks, using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species (in total 133 taxa; not all loci available for all species). We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling (in total 51 samples of 44 taxa across 40 species). Our results confirm the previous findings of rampant morphological convergence and divergence, and reveal new cases of paraphyletic genera. We propose a new subfamily classification, and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae. Our study supports recently proposed species splits as well as some recent lumps, while also questioning some of the latter. This comprehensive phylogeny will form an important basis for future studies, such as comparative studies of lark natural history, ecology, evolution and conservation.

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    fulltext
  • 20.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rasmussen, Pamela C.
    Delicate Prinia (Prinia lepida)2022Other (Other academic)
  • 21.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci, Swedish Species Informat Ctr, Box 7007, SE-75007 Uppsala, Sweden.;Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China..
    Rasmussen, Pamela C.
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48864 USA.;Michigan State Univ, MSU Museum, E Lansing, MI 48864 USA.;Nat Hist Museum, Nat Hist Museum Tring, Bird Grp, Akeman St, Tring HP23 6AP, England..
    Sangster, George
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, POB 50007, SE-10405 Stockholm, Sweden.;Naturalis Biodivers Ctr, Darwinweg 4, NL-2333 CR Leiden, Netherlands..
    Dalvi, Shashank
    GKVK, Natl Ctr Biol Sci, Researchers Wildlife Conservat, F-21,Bellary Rd, Bengaluru 560065, Karnataka, India..
    Round, Philip D.
    Mahidol Univ, Fac Sci, Dept Biol, Rama 6 Rd, Bangkok 10400, Thailand..
    Zhang, Ruiying
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China..
    Yao, Cheng-Te
    COA, Endem Species Res Inst, High Altitude Expt Stn, Chi Chi, Taiwan..
    Irestedt, Martin
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, POB 50007, SE-10405 Stockholm, Sweden..
    Le Manh, Hung
    Grad Univ Sci & Technol, Vietnam Acad Sci & Technol, Inst Ecol & Biol Resources, 18 Hoang Quoc Viet, Hanoi, Vietnam..
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China..
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Systemat & Biodivers, Box 463, SE-40530 Gothenburg, Sweden..
    Multiple species within the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex revealed through an integrative taxonomic approach2020In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 162, no 3, p. 936-967Article in journal (Refereed)
    Abstract [en]

    We re-evaluated the taxonomy of the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age-related, geographical and taxon-specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses have focused on this group, misinterpretation of taxonomic signals from limited conventional morphological study alone was likely. Using mitochondrial and nuclear DNA, we found that P. crinigera sensu lato (s.l.) comprises two non-sister groups of taxa (Himalayan crinigera and Chinese striata groups) that differ substantially morphologically and vocally and that are broadly sympatric in Yunnan Province, China. Prinia polychroa cooki (Myanmar) and P. p. rocki (southern Vietnam) are each morphologically, vocally and genetically distinct. Thai, Cambodian and Laotian populations formerly ascribed to P. p. cooki are morphologically and vocally most similar to and most closely related to Javan P. p. polychroa, and require a new name, proposed here. Prinia p. bangsi of Yunnan is part of the crinigera group rather than of P. polychroa, and hence there is no evidence for sympatry between P. polychroa s.l. and P. crinigera s.l., nor of the occurrence of P. polychroa in mainland China or Taiwan. We recommend the recognition of five species in the complex, with the following suggestions for new English names: Himalayan Prinia P. crinigera sensu stricto (s.s.; with subspecies striatula, crinigera, yunnanensis and bangsi); Chinese Prinia P. striata (subspecies catharia, parumstriata and striata); Burmese Prinia P. cooki (monotypic); Annam Prinia P. rocki (monotypic) and Deignan's Prinia P. polychroa s.s. (subspecies Javan polychroa and the new Southeast Asian taxon). This study underlines the importance of using multiple datasets for the elucidation of diversity of cryptic bird species and their evolutionary history and biogeography.

  • 22.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci SLU, Swedish Species Informat Ctr, Box 7007, S-75007 Uppsala, Sweden; Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Rasmussen, Pamela C.
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48864 USA;Michigan State Univ, MSU Museum, E Lansing, MI 48864 USA;Nat Hist Museum Tring, Bird Grp, Akeman St, Tring HP23 6AP, England.
    Xia, Canwei
    Beijing Normal Univ, Minist Educ, Coll Life Sci, Key Lab Biodivers & Ecol Engn, Beijing 100875, Peoples R China.
    Gelang, Magnus
    Gothenburg Nat Hist Museum, Box 7283, S-40235 Gothenburg, Sweden.
    Liu, Yang
    Sun Yat Sen Univ, Sch Life Sci, Dept Ecol, State Key Lab Biocontrol, Guangzhou 510275, Guangdong, Peoples R China.
    Chen, Guoling
    Sun Yat Sen Univ, Sch Life Sci, Dept Ecol, State Key Lab Biocontrol, Guangzhou 510275, Guangdong, Peoples R China.
    Zhao, Min
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China;Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
    Hao, Yan
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China;Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
    Zhao, Chao
    Cloud Mt Conservat, Dali 671003, Yunnan, Peoples R China.
    Zhao, Jian
    Sun Yat Sen Univ, Sch Life Sci, Dept Ecol, State Key Lab Biocontrol, Guangzhou 510275, Guangdong, Peoples R China.
    Yao, Chengte
    COA, Endem Species Res Inst, High Altitude Expt Stn, Chi Chi 55244, Taiwan.
    Eaton, James A.
    Birdtour Asia, 17 Keats Ave, Derby DE23 4EE, England.
    Hutchinson, Robert
    Birdtour Asia, 17 Keats Ave, Derby DE23 4EE, England.
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Systemat & Biodivers, Box 463, S-40530 Gothenburg, Sweden.
    Taxonomy of the White-browed Shortwing (Brachypteryx montana) complex on mainland Asia and Taiwan: an integrative approach supports recognition of three instead of one species2018In: Avian Research, ISSN 0005-2175, E-ISSN 2053-7166, Vol. 9, article id 34Article in journal (Refereed)
    Abstract [en]

    Background: The White-browed Shortwing (Brachypteryx montana) is widespread from the central Himalayas to the southeast Chinese mainland and the island of Taiwan, the Philippines and Indonesia. Multiple subspecies are recognised, and several of these have recently been suggested to be treated as separate species based on differences in morphology and songs.

    Methods: We here analyse plumage, morphometrics, songs, two mitochondrial and two nuclear markers, and geographical distributions of the two mainland Asian taxa B. m. cruralis and B. m. sinensis and the Taiwanese B. m. goodfellowi.

    Results: We conclude that these differ congruently in morphology, songs and DNA. Male B. m. goodfellowi is the most divergent in plumage (sexually monomorphic, unlike the two others; male similar to female), and B. m. cruralis and B. m. sinensis differ in male plumage maturation. The song of B. m. cruralis is strongly divergent from the others, whereas the songs of B. m. sinensis and B. m. goodfellowi are more similar to each other. Brachypteryx m. sinensis and B. m. goodfellowi are sisters, with an estimated divergence time 4.1 million years ago (mya; 95% highest posterior distribution [HPD] 2.8-5.5mya), and B. m. cruralis separated from these two 5.8mya (95% HPD 4.1-7.5mya). We also report notable range extensions of B. m. sinensis as well as sympatry between this taxon and B. m. cruralis in Sichuan Province, China. Brachypteryx m. montana from Java is found to be more closely related to Lesser Shortwing (B. leucophris) and Rusty-bellied Shortwing (B. hyperythra) than to the mainland Asian and Taiwanese taxa.

    Conclusion: Our data support a recent proposal to treat the three mainland Asian and Taiwanese taxa as three species, separate from B. montana sensu stricto: B. cruralis (central Himalayas to south central China and south Vietnam), B. sinensis (north central to southeastern part of mainland China) and B. goodfellowi (Taiwan Island).

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  • 23.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China..
    Rasmussen, Pamela C.
    Michigan State Univ, Dept Integrat Biol, E Lansing, MI 48824 USA.;Michigan State Univ, MSU Museum, E Lansing, MI 48824 USA.;Nat Hist Museum, Bird Grp, Tring, England..
    Xia, Canwei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Beijing Normal Univ, Coll Life Sci, Key Lab Biodivers Sci & Ecol Engn, Minist Educ, Beijing, Peoples R China..
    Zhang, Lijun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Liu, Chengyi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Magnusson, Jesper
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Shafaeipour, Arya
    Univ Yasuj, Fac Sci, Dept Biol, Yasuj, Iran..
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Systemat & Biodivers, Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Gothenburg, Sweden..
    Morphology, vocalizations, and mitochondrial DNA suggest that the Graceful Prinia is two species2021In: The AUK: A Quarterly Journal of Ornithology, ISSN 0004-8038, E-ISSN 1938-4254, Vol. 138, no 2, article id ukab014Article in journal (Refereed)
    Abstract [en]

    Prinias (Cisticolidae:Prinia) are resident warblers of open areas across Africa and Asia and include many polytypic species whose species limits have not been seriously reevaluated recently. Based on an integrative taxonomic analysis of morphology, song, and mitochondrial DNA (mtDNA), we suggest that 2 species should be recognized in the Graceful Prinia (Prinia gracilis) complex. In addition, our morphological analyses show the existence of a well-marked undescribed form in southeastern Somalia, which we name herein as a new subspecies. Prinia gracilisis a small, drab, long-tailed species with streaking above and plain pale underparts that has been suggested to fall into 2 groups: the southwestern nominate group (from Egypt to Oman) and the northeastern lepida group (from Turkey through India). However, the characters presented to justify this grouping are variable and show a mosaic pattern, and whether genetic and vocal differences exist is unknown. We found consistent between-group song differences, with the nominate group giving consistently longer inter-phrase intervals, whereas the members of the lepida group sing an essentially continuous reel. An mtDNA tree suggests a deep split between the nominate and lepida groups, with a coalescence time between these clades of similar to 2.2 million years ago. Vocal and mtDNA analyses provided evidence that the northeastern Arabian Peninsula taxon carpenteri belongs to the lepida group. We found that, of all the morphological characters proposed, only proportions and tail barring and spotting relatively consistently distinguish the 2 groups. However, these characters strongly suggest that the eastern Arabian Peninsula is populated by taxa of both the gracilis and lepida groups, in different areas, but we lack genetic and bioacoustic data to corroborate this. Although further study is needed in potential contact zones, we suggest that 2 species should be recognized in the P. gracilis complex, and we propose the retention of the English name Graceful Prinia for P. gracilis sensu stricto, while we suggest that P. lepida be known as Delicate Prinia.

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  • 24.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci SLU, Swedish Species Informat Ctr, Box 7007, SE-75007 Uppsala, Sweden;Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Rheindt, Frank E.
    Natl Univ Singapore, Dept Biol Sci, 16 Sci Dr 4, Singapore 117558, Singapore.
    Zhang, Ruiying
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Zhao, Min
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Wang, Jing
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Zhu, Xiaojia
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Gwee, Chyi Yin
    Natl Univ Singapore, Dept Biol Sci, 16 Sci Dr 4, Singapore 117558, Singapore.
    Hao, Yan
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Ohlson, Jan
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Box 50007, SE-10405 Stockholm, Sweden.
    Jia, Chenxi
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Prawiradilaga, Dewi M.
    Indonesian Inst Sci LIPI, Cibinong Sci Ctr, Res Ctr Biol, Jalan Raya Jakarta Bogor KM 46, Bogor 16911, Indonesia.
    Ericson, Per G. P.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Box 50007, SE-10405 Stockholm, Sweden.
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing 100101, Peoples R China.
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, SE-40530 Gothenburg, Sweden.
    Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 126, p. 141-152Article in journal (Refereed)
    Abstract [en]

    The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment, and we argue against proliferation of taxonomic names, and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.

  • 25.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ryan, Peter
    Horsfield's Bushlark (Mirafra javanica)2022Other (Other academic)
  • 26.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sundev, Gombobaatar
    Donald, Paul F.
    Asian Short-toed Lark (Alaudala cheleensis)2023Other (Other academic)
  • 27.
    Alström, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China..
    van Linschooten, Jip
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Donald, Paul F.
    Univ Cambridge, Dept Zool, Downing St, Cambridge CB2 3EJ, England..
    Sundev, Gombobaatar
    Natl Univ Mongolia, POB 537,Ulaanbaatar 210646a, Ulaanbaatar, Mongolia.;Mongolian Ornithol Soc, POB 537,Ulaanbaatar 210646a, Ulaanbaatar, Mongolia..
    Mohammadi, Zeinolabedin
    Ferdowsi Univ Mashhad, Fac Sci, Inst Appl Zool, Dept Biol, Mashhad, Razavi Khorasan, Iran.;Ferdowsi Univ Mashhad, Fac Sci, Inst Appl Zool, Res Dept Zool Innovat, Mashhad, Razavi Khorasan, Iran..
    Ghorbani, Fatemeh
    Ferdowsi Univ Mashhad, Fac Sci, Inst Appl Zool, Dept Biol, Mashhad, Razavi Khorasan, Iran.;Ferdowsi Univ Mashhad, Fac Sci, Inst Appl Zool, Res Dept Zool Innovat, Mashhad, Razavi Khorasan, Iran..
    Shafaeipour, Arya
    Univ Yasuj, Fac Sci, Dept Biol, Yasuj, Iran..
    van den Berg, Arnoud
    Sound Approach, Duinlustparkweg 98, NL-2082 EG Santpoort Zuid, Netherlands..
    Robb, Magnus
    Sound Approach, Rua Dr Pedro Almeida Lima 6, P-2710122 Sintra, Portugal..
    Aliabadian, Mansour
    Ferdowsi Univ Mashhad, Fac Sci, Inst Appl Zool, Dept Biol, Mashhad, Razavi Khorasan, Iran.;Ferdowsi Univ Mashhad, Fac Sci, Inst Appl Zool, Res Dept Zool Innovat, Mashhad, Razavi Khorasan, Iran..
    Wei, Chentao
    Sun Yat Sen Univ, Sch Life Sci, Dept Ecol, State Key Lab Biocontrol, Guangzhou 510275, Peoples R China..
    Lei, Fumin
    Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China..
    Oxelman, Bengt
    Univ Gothenburg, Dept Biol & Environm Sci, Systemat & Biodivers, Box 463, SE-40530 Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Box 461, SE-40530 Gothenburg, Sweden..
    Olsson, Urban
    Univ Gothenburg, Dept Biol & Environm Sci, Systemat & Biodivers, Box 463, SE-40530 Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Box 461, SE-40530 Gothenburg, Sweden..
    Multiple species delimitation approaches applied to the avian lark genus Alaudala2021In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 154, article id 106994Article in journal (Refereed)
    Abstract [en]

    Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.

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  • 28.
    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.

  • 29.
    Ament-Velásquez, Sandra Lorena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Giraud, Tatiana
    Univ Paris Saclay, AgroParisTech, CNRS, Ecol Systemat Evolut, F-91400 Orsay, France.
    Debuchy, Robert
    Univ Paris Saclas CEA, Inst Integrat Biol Cell I2BC, CNRS, F-91198 Gif Sur Yvette, France.
    Saupe, Sven J.
    Univ Bordeaux, IBGC, UMR 5095, CNRS, 1 Rue Camille St Saens, F-33077 Bordeaux, France.
    Debets, Alfons J. M.
    Wageningen Univ, Lab Genet, Arboretumlaan 4, NL-6703 BD Wageningen, Netherlands.
    Bastiaans, Eric
    Wageningen Univ, Lab Genet, Arboretumlaan 4, NL-6703 BD Wageningen, Netherlands.
    Malagnac, Fabienne
    Univ Paris Saclas CEA, Inst Integrat Biol Cell I2BC, CNRS, F-91198 Gif Sur Yvette, France.
    Grognet, Pierre
    Univ Paris Saclas CEA, Inst Integrat Biol Cell I2BC, CNRS, F-91198 Gif Sur Yvette, France.
    Peraza-Reyes, Leonardo
    Univ Nacl Autonoma Mexico, Inst Fisiol Celular, Dept Bioquim & Biol Estruct, Mexico City, DF, Mexico.
    Gladieux, Pierre
    Univ Montpellier, Inst Agro, CIRAD, INRAE,UMR BGPI, F-34398 Montpellier, France.
    Kruys, Åsa
    Uppsala University, Music and Museums, Museum of Evolution.
    Silar, Philippe
    Univ Paris, Lab Interdisciplinaire Energies Demain LIED, F-75006 Paris, France.
    Huhndorf, Sabine M.
    Bot Dept, Field Museum, Chicago, IL 60605 USA.
    Miller, Andrew N.
    Univ Illinois, Illinois Nat Hist Survey, Champaign, IL 61820 USA.
    Vogan, Aaron A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The taxonomy of the model filamentous fungus Podospora anserina2020In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 75, p. 51-69Article in journal (Refereed)
    Abstract [en]

    The filamentous fungus Podospora anserina has been used as a model organism for more than 100 years and has proved to be an invaluable resource in numerous areas of research. Throughout this period, P. anserina has been embroiled in a number of taxonomic controversies regarding the proper name under which it should be called. The most recent taxonomic treatment proposed to change the name of this important species to Triangularia anserina. The results of past name changes of this species indicate that the broader research community is unlikely to accept this change, which will lead to nomenclatural instability and confusion in literature. Here, we review the phylogeny of the species closely related to P. anserina and provide evidence that currently available marker information is insufficient to resolve the relationships amongst many of the lineages. We argue that it is not only premature to propose a new name for P. anserina based on current data, but also that every effort should be made to retain P. anserina as the current name to ensure stability and to minimise confusion in scientific literature. Therefore, we synonymise Triangularia with Podospora and suggest that either the type species of Podospora be moved to P. anserina from P. fimiseda or that all species within the Podosporaceae be placed in the genus Podospora.

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  • 30.
    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.

  • 31.
    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.

  • 32.
    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.

  • 33.
    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.

  • 34.
    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)
  • 35.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Genetiska fingeravtryck löser gåtan med Linnés växter?2018In: Fauna och flora, ISSN 0014-8903, Vol. 113, no 2, p. 2-5Article in journal (Other (popular science, discussion, etc.))
  • 36.
    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)
  • 37.
    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)
  • 38.
    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.

  • 39.
    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)
  • 40. 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)
  • 41.
    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.

  • 42.
    Aïgnon, Hyppolite L.
    et al.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Plants Soil Fungi Interact, Parakou, Benin..
    Fan, Yu-Guang
    Hainan Med Univ, Sch Pharm, Trop Environm & Hlth Lab, Key Lab Trop Translat Med,Minist Educ, Haikou, Peoples R China..
    De Kesel, André
    Meise Bot Garden, Meise, Belgium..
    Bahram, Mohammad
    Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Yorou, Nourou S.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Plants Soil Fungi Interact, Parakou, Benin..
    A new species of Inosperma, and first record of I. afromelliolens (Inocybaceae, Fungi) from West Africa2023In: PLOS ONE, E-ISSN 1932-6203, Vol. 18, no 10, article id e0290894Article in journal (Refereed)
    Abstract [en]

    Here, we present the newly identified Inosperma macrocarpa and the first record of I. afromelliolens from West Africa. Inosperma macrocarpa is nested in an Old World Tropical clade, based on a molecular phylogeny inferred from the sequences of ITS, LSU, RPB2, and TEF1. Complete descriptions and illustrations, including photographs and line drawings, of the new species are presented. Morphological and molecular analyses based on collections from Benin confirmed the presence of I. afromelliolens in West Africa. Toxicity analysis showed that neither species contained muscarine, which further supports the hypothesis that the ability to produce muscarine is a derived trait of Inosperma.

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  • 43. 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)
  • 44.
    Badou, Sylvestre A.
    et al.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    De Kesel, Andre
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium.
    Raspe, Olivier
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium;Federat Wallonie Bruxelles, Rue A Lavallee 1, B-1080 Brussels, Belgium.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Guelly, Atsu K.
    Univ Lome, Fac Sci, Dept Bot & Ecol Vegetale, BP1515, Lome, Togo.
    Yorou, Nourou S.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    Two new African siblings of Pulveroboletus ravenelii (Boletaceae)2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 43, p. 115-130Article in journal (Refereed)
    Abstract [en]

    This paper sorts out the taxonomy of species affiliated with Pulveroboletus ravenelii in the Guineo-soudanian and Zambezian woodlands of Africa. Morphological and genetic characters of African Pulveroboletus collections were studied and compared to those of North American and Asian species. A phylogenetic analysis showed that the African specimens form a subclade, sister to the Asian and American taxa. Although clamp connections have previously never been reported from Pulveroboletus, all specimens of the African subclade show very small clamp connections. Two new African species, Pulveroboletus africanus sp. nov. and P. sokponianus sp. nov., are described and illustrated. Comments concerning morphology and identification, as well as distribution and ecology, are given for both species.

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    FULLTEXT01
  • 45. Badou, Sylvestre A.
    et al.
    Furneaux, Brendan R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    De Kesel, André
    Kalsoom, Faheema
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Houdanon, Roel D.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Yorou, Nourou S.
    Paxilloboletus gen. nov., a new lamellate bolete genus from tropical Africa2022In: Mycological progress, ISSN 1617-416X, E-ISSN 1861-8952, Vol. 21, no 1, p. 243-256Article in journal (Refereed)
    Abstract [en]

    This study presents Paxilloboletus gen. nov., a new lamellate bolete genus represented by two tropical African species, Paxilloboletus africanus sp. nov. and Paxilloboletus latisporus sp. nov. Although the new taxa strongly resemble Paxillus (Paxillaceae), they lack clamp connections and form a separate generic clade within the Boletaceae phylogeny. The new species are lookalikes, morphologically only separable by their spore morphology. Descriptions and illustrations of the new genus and new species are given, as well as comments on ecology, distribution, and morphological differences with other gilled Boletaceae.

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    fulltext
  • 46.
    Baiao, Guilherme Costa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Swedish Museum Nat Hist, Dept Zool, Stockholm, Sweden.
    Forshage, Mattias
    Swedish Museum Nat Hist, Dept Zool, Stockholm, Sweden.
    Revision of the West Palaearctic species of Rhoptromeris Forster, 1869 (Hymenoptera: Figitidae: Eucoilinae)2018In: Journal of Natural History, ISSN 0022-2933, E-ISSN 1464-5262, Vol. 52, no 17-18, p. 1201-1224Article in journal (Refereed)
    Abstract [en]

    The West Palearctic species of Rhoptromeris are revised. A total of 11 species are recognised as valid in this region, including four newly described species: Rhoptromeris dichromata sp. nov., Rhoptromeris koponeni sp. nov., Rhoptromeris leptocornis sp. nov. and Rhoptromeris macaronesiensis sp. nov. Eucoila luteicornis Ionescu, 1959 is synonymised with Rhoptromeris heptoma (Hartig, 1840) syn. nov. A checklist of the Holarctic Rhoptromeris is presented and an identification key to the West Palearctic species is provided.

    www.zoobank.org/urn:lsid:zoobank.org:pub:8164332C-93E2-4E3F-A408-F5FF5DFB366E

    Download full text (pdf)
    fulltext
  • 47.
    Baldauf, Sandra L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Department of Organismal Biology, Uppsala University Program in Systematic Biology, , Uppsala 75236, Sweden.
    Al Jewari, Caesar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Department of Organismal Biology, Uppsala University Program in Systematic Biology, , Uppsala 75236, Sweden.
    Widespread mosaicism in eukaryotic genes of bacterial ancestryManuscript (preprint) (Other academic)
  • 48.
    Baldauf, Sandra L.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fiz-Palacios, Omar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A Deep Hidden Diversity of Dictyostelia2018In: Protist, ISSN 1434-4610, E-ISSN 1618-0941, Vol. 169, no 1, p. 64-78Article in journal (Refereed)
    Abstract [en]

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

  • 49. 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: German Journal of Herpetology, ISSN 0036-3375, Vol. 44, no 1, p. 59-62Article in journal (Refereed)
  • 50. 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)
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