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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.

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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. Abalaka, J. L.
    et al.
    Ottosson, Ulf
    Tende, Talatu
    Larson, Keith W.
    Rock Firefinch Lagonosticta sanguinodorsalis in the Mandara Mountains, north-east Nigeria: a new subspecies?2010In: African Bird Club Bulletin, ISSN 1352-481X, Vol. 17, no 2, p. 210-211Article in journal (Refereed)
    Abstract [fr]

    L’Amarante des rochers Lagonosticta sanguinodorsalis dans les Monts Mandara, Nigeria du sud-est: une nouvelle sous-espèce ? Nous fournissons une description d’un mâle et d’une femelle, ainsi que desphotos d’un mâle, d’un amarante capturé dans les Monts Mandara, au nord-est du Nigeria. Le plumage et le cri de cet amarante sont identiques à ceux de l’Amarante des rochers Lagonosticta sanguinodorsalis, une espèce précédemment rapportée de la zone, excepté que le mâle n’a pas la couronne grise typique de l’espèce. Des travaux supplémentaires sur le terrain sont nécessaires pour déterminer s’il agit d’un individu aberrant ou d’une population de l’Amarante des rochers morphologiquement distincte.

  • 4.
    Abalde, Samuel
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Crocetta, Fabio
    Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
    Tenorio, Manuel J.
    Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain.
    D'Aniello, Salvatore
    Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy.
    Fassio, Giulia
    Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Zoology–Viale dell’Università 32, 00185 Rome, Italy.
    Rodríguez-Flores, Paula C.
    Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
    Uribe, Juan E.
    Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
    Afonso, Carlos M.L.
    Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal.
    Oliverio, Marco
    Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Zoology–Viale dell’Università 32, 00185 Rome, Italy.
    Zardoya, Rafael
    Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
    Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus2023In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 186, p. 107838-107838, article id 107838Article in journal (Refereed)
    Abstract [en]

    The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.

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  • 5.
    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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  • 6.
    Ahlberg, Louise
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Molecular sexing and species determination of the Sylvia cantillans complex.2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Abstract

    The Sylvia cantillans complex is a collection of closely related passerine birds including three species (S. cantillans, S. subalpina and S. inornata) that are further subdivided into four subspecies (S. c. cantillans, S. c. albistriata, S. i. inornata, S. i. iberiae). All taxa in the complex are morphologically similar and difficult to discern from each other based on plumage. Furthermore, sexing birds is also difficult as females and males without breeding plumage are almost identical. In this study I used molecular methods to identify S. cantillans complex birds in order to compare field-based and molecular observations. DNA was extracted from a set of feathers collected from S. cantillans complex birds from Italy to determine species, based on mitochondrial gene cytochrome b sequences. The sex was determined using PCR amplicon profiles of CHD1W and CHD1Z genes that differ in size between males and females. The cytochrome b amplification was successful in all feathers and CHD1W and CHD1Z in all but two. The molecular work was compared with the results of phenotypic identification made by ringers and expert ornithologists. The experts on average, identified the correct species in 51% of the warblers, and sex 66% and 64% for females and males respectively. This highlights that molecular methods are highly effective to determine species and sex and that they are more reliable than identification by plumage alone. This is important to keep in mind in studies of diversity and conservation to avoid underestimating the number of species and the sex of individuals involved, which might cause more harm than good.

  • 7.
    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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  • 8.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology. Harper Adams University.
    Back, Matthew
    Prior, Thomas
    Karssen, Gerrit
    Lawson, Rebecca
    Adams, Ian
    Sapp, Melanie
    Metabarcoding of soil nematodes: the importance of taxonomiccoverage and availability of reference sequences in choosingsuitable marker(s)2019In: Metabarcoding and Metagenomics, Vol. 3, p. 77-99Article in journal (Refereed)
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  • 9. Ahti, Teuvo
    et al.
    Mayrhofer, Helmut
    Schultz, Matthias
    Tehler, Anders
    Swedish Museum of Natural History, Department of Botany.
    Fryday, Alan M
    First supplement to the lichen checklist of South Africa2016In: Bothalia, African Biodiversity & Conservation Journal, Vol. 46, no 1Article in journal (Refereed)
  • 10.
    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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  • 11.
    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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  • 12.
    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.

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  • 13.
    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.

  • 14.
    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.

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  • 15.
    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.

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  • 16.
    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.

  • 17.
    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)
  • 18. ALARIE, YVES
    et al.
    MICHAT, MARIANO C.
    Bergsten, Johannes
    Swedish Museum of Natural History, Department of Zoology.
    HÁJEK, JIŘÍ
    Morphology of the larvae of Rhantaticus congestus (Klug, 1833) and phylogenetic comparison with other known Aciliini (Coleoptera: Dytiscidae: Dytiscinae)2023In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 5380, no 3, p. 247-264Article in journal (Refereed)
    Abstract [en]

    We describe the second- and third instar larvae of the diving beetle Rhantaticus congestus (Klug, 1833), including detailed morphometric and chaetotaxic analyses of the cephalic capsule, head appendages, legs, terminal abdominal segment and urogomphi in order to discover useful characters for distinguishing Rhantaticus Sharp, 1882 larvae from those of other known Aciliini (Coleoptera: Dytiscidae: Dytiscinae). A parsimony analysis based on 94 larval characteristics of nine Aciliini species in five genera (Acilius Leach, 1817, Graphoderus Dejean, 1833, Rhantaticus, Sandracottus Sharp, 1882, Thermonectus Dejean, 1833) was conducted using the program TNT. Rhantaticus shares with all these genera several larval character states which support its inclusion in the Aciliini. Whereas Rhantaticus larva stands out from other known genera by several unique character states, our parsimony analysis did not recover any clear phylogenetic position of this genus within the Aciliini.

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  • 19. ALARIE, YVES
    et al.
    MICHAT, MARIANO C.
    RANARILALATIANA, TOLOTRA
    Bergsten, Johannes
    Swedish Museum of Natural History, Department of Zoology.
    Larval morphology of the Madagascan endemic diving beetle genus Hovahydrus Biström, 1982 (Coleoptera: Dytiscidae) and phylogenetic comparison with other known Hyphydrini2022In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 5219, no 3, p. 227-246Article in journal (Refereed)
    Abstract [en]

    We describe for the first time the instar III larva of the diving beetle genus Hovahydrus Biström, 1982, based on H. praetextus (Guignot, 1951) and a new species yet to be described (identified here as Hovahydrus sp. near H. minutissimus (Régimbart, 1903)). We include detailed morphometric and chaetotaxic analyses of the cephalic capsule, head appendages, legs, last abdominal segment and urogomphi in order to discover useful characters for distinguishing Hovahydrus larvae from those of other known Hyphydrini (Coleoptera: Dytiscidae, Hydroporinae). A provisional parsimony analysis based on larval characteristics of 11 Hyphydrini species in eight genera was conducted using the program TNT. Larval morphology supports a close relationship between Hovahydrus, Hyphydrus Illiger, 1802, and the endemic South Africa genera Andex Sharp, 1882, Coelhydrus Sharp, 1882, Darwinhydrus Sharp, 1882 and Primospes Sharp, 1882. 

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  • 20. Aliabadian, Mansour
    et al.
    Kaboli, Mohammad
    Foerschler, Marc I.
    Nijman, Vincent
    Chamani, Atefeh
    Tillier, Annie
    Prodon, Roger
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zuccon, Dario
    Erratum to: Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae) (vol 65, pg 35, 2012)2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, no 3, p. 1017-1019Article in journal (Refereed)
  • 21. Aliabadian, Mansour
    et al.
    Kaboli, Mohammad
    Förschler, Marc I
    Nijman, Vincent
    Chamani, Atefeh
    Tillier, Annie
    Prodon, Roger
    Pasquet, Eric
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Zuccon, Dario
    Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae).2012In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 65, no 1, p. 35-45Article in journal (Refereed)
    Abstract [en]

    Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular phylogenetic analysis of this group to date, with a complete taxon sampling at the species level. The analysis, based on a multilocus dataset including three mitochondrial and three nuclear loci, allows us to elucidate the phylogenetic relationships and test the traditional generic limits. All genera are non-monophyletic, suggesting extensive convergence on similar plumage patterns in unrelated species. While the colour pattern appear to be a poor predictor of the phylogenetic relationships, some of the ecological and behavioural traits agree relatively well with the major clades. Following our results, we also propose a revised generic classification for the whole group.

  • 22. Alonso, Marta
    et al.
    Jiménez, Juan A.
    Nylinder, Stephan
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Cano, Maria J.
    Disentangling generic limits in Chionoloma, Oxystegus, Pachyneuropsis and Pseudosymblepharis (Bryophyta: Pottiaceae): An inquiry into their phylogenetic relationships2016In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 65, p. 3-18Article in journal (Refereed)
  • 23. Alstrom, Per
    et al.
    Olsson, Urban
    Rasmussen, Pamela C.
    Yao, Cheng-Te
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Sundberg, Per
    Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae)2007In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 149, no 3, p. 437-452Article in journal (Refereed)
  • 24. 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.

  • 25. 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)
  • 26. Alström, Per
    et al.
    Cibois, Alice
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Zuccon, Dario
    Gelang, Magnus
    Fjeldså, Jon
    Andersen, Michael J.
    Moyle, Robert G.
    Pasquet, Eric
    Olsson, Urban
    Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification2018In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 127, p. 367-375Article in journal (Refereed)
    Abstract [en]

    The widespread Old World avian family Locustellidae (‘grassbirds and allies’) comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a clade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.

  • 27.
    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)
  • 28.
    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)
  • 29.
    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)
  • 30. Alström, Per
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Olsson, Urban
    Sundberg, Per
    Phylogeny and classification of the avian superfamily Sylvioidea.2006In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 38, no 2, p. 381-97Article in journal (Refereed)
    Abstract [en]

    Sylvioidea is one of the three superfamilies recognized within the largest avian radiation, the parvorder Passerida. In the present study, which is the first taxon-dense analysis of the Sylvioidea based on sequence data (nuclear myoglobin intron II and mitochondrial cytochrome b gene), we investigate the interrelationships among the four "sylvioid" clades found by previous workers, as well as the relationships within the largest of these clades. The nuclear and mitochondrial loci estimate basically the same phylogeny, with minor differences in resolution. The trees based on myoglobin and the combined data identify a strongly supported clade that includes the taxa previously allocated to Sylvioidea, except for Sitta (nuthatches), Certhia (treecreepers), Parus (tits), Remiz (penduline tits), Troglodytes and Campylorhynchus (wrens), Polioptila (gnatcatchers), and Regulus (crests/kinglets); this clade also comprises larks, which have previously been placed in the superfamily Passeroidea. We refer to this clade as Sylvioidea. This clade is further divided into 10 main, well-supported clades, which we suggest form the basis for a revised classification.

  • 31. Alström, Per
    et al.
    Fregin, Silke
    Norman, Janette A
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Christidis, Les
    Olsson, Urban
    Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae.2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 58, no 3, p. 513-26Article in journal (Refereed)
    Abstract [en]

    The phylogeny of most of the species in the avian passerine family Locustellidae is inferred using a Bayesian species tree approach (Bayesian Estimation of Species Trees, BEST), as well as a traditional Bayesian gene tree method (MrBayes), based on a dataset comprising one mitochondrial and four nuclear loci. The trees inferred by the different methods agree fairly well in topology, although in a few cases there are marked differences. Some of these discrepancies might be due to convergence problems for BEST (despite up to 1×10(9) iterations). The phylogeny strongly disagrees with the current taxonomy at the generic level, and we propose a revised classification that recognizes four instead of seven genera. These results emphasize the well known but still often neglected problem of basing classifications on non-cladistic evaluations of morphological characters. An analysis of an extended mitochondrial dataset with multiple individuals from most species, including many subspecies, suggest that several taxa presently treated as subspecies or as monotypic species as well as a few taxa recognized as separate species are in need of further taxonomic work.

  • 32. Alström, Per
    et al.
    Höhna, Sebastian
    Gelang, Magnus
    Swedish Museum of Natural History, Department of Zoology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Olsson, Urban
    Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset.2011In: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 11, p. 352-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species.

    RESULTS: There are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods).

    CONCLUSIONS: The molecular phylogeny presented here is strongly inconsistent with the traditional, morphology-based classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the well-known but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories.

  • 33. Alström, Per
    et al.
    Jønsson, Knud A.
    Fjeldså, Jon
    Ödeen, Anders
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Irestedt, Martin
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dramatic niche shifts and morphological change in two insular bird species2015In: Royal Society Open Science, ISSN 2054-5703, Vol. 2, article id 140364Article in journal (Refereed)
    Abstract [en]

    Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.

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  • 34.
    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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  • 35.
    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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  • 36.
    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)
  • 37.
    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.

  • 38.
    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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  • 39.
    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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  • 40.
    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.

  • 41.
    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)
  • 42.
    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)
  • 43.
    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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  • 44. Alström, Per
    et al.
    Zhang, R
    Zhao, M
    Wang, J
    Zhu, X
    Gwee, C.H.
    Hao, Y
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Jia, C
    Prawiradilaga, D M
    Ericson, Per G P
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Lei, Fumin
    Olsson, Urban
    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)
  • 45.
    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.

  • 46.
    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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  • 47.
    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.

  • 48.
    Anderberg, Arne A.
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Eldenäs, Pia
    Laboratory for Molecular Systematics, Swedish Museum of Natural History.
    Bayer, Randall J.
    Australian National Herbarium, Centre for Plant Biodiversity Research.
    Englund, Markus
    Stockholm University, Faculty of Science, Department of Botany.
    Evolutionary relationships in the Asteraceae tribe Inuleae (incl. Plucheeae) evidenced by DNA sequences of ndhF; with notes on the systematic positions of some aberrant genera2005In: Organisms Diversity & Evolution, ISSN 1439-6092, E-ISSN 1618-1077, Vol. 5, no 2, p. 135-146Article in journal (Refereed)
    Abstract [en]

    The phylogenetic relationships between the tribes Inuleae sensu stricto and Plucheeae are investigated by analysis of sequence data from the cpDNA gene ndhF. The delimitation between the two tribes is elucidated, and the systematic positions of a number of genera associated with these groups, i.e. genera with either aberrant morphological characters or a debated systematic position, are clarified. Together, the Inuleae and Plucheeae form a monophyletic group in which the majority of genera of Inuleae s.str. form one clade, and all the taxa from the Plucheeae together with the genera Antiphiona, Calostephane, Geigeria, Ondetia, Pechuel-loeschea, Pegolettia, and Iphionopsis from Inuleae s.str. form another. Members of the Plucheeae are nested with genera of the Inuleae s.str., and support for the Plucheeae clade is weak. Consequently, the latter cannot be maintained and the two groups are treated as one tribe, Inuleae, with the two subtribes Inulinae and Plucheinae. The genera Asteriscus, Chrysophthalmum, Inula, Laggera, Pentanema, Pluchea, and Pulicaria are demonstrated to be non-monophyletic. Cratystylis and Iphionopsis are found to belong to the same clade as the taxa of the former Plucheeae. Caesulia is shown to be a close relative of Duhaldea and Blumea of the Inuleae-Inulinae. The genera Callilepis and Zoutpansbergia belong to the major clade of the family that includes the tribes Heliantheae sensu lato and Inuleae (incl. Plucheeae), but their exact position remains unresolved. The genus Gymnarrhena is not part of the Inuleae, but is either part of the unresolved basal complex of the paraphyletic Cichorioideae, or sister to the entire Asteroideae.

  • 49.
    Anderberg, Arne A.
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Englund, Markus
    Stockholm University, Faculty of Science, Department of Botany.
    Beentje, Henk
    On the systematic position of Inula rungwensis2008In: Compositae Newsletter, ISSN 0284-8422, Vol. 46, p. 83-84Article in journal (Other academic)
    Abstract [en]

    The systematic position of Inula rungwensis Beentje is discussed. It is concluded that it is conspecific with Gerbera piloselloides (L.) Cass. of the tribe Mutisieae.

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  • 50. Anderberg, Arne A.
    et al.
    Rydin, Catarina
    Stockholm University, Faculty of Science, Department of Botany.
    Källersjö, Mari
    Phylogenetic relationships in the order Ericales s.l.: analyses of molecular data from five genes from the plastid and mitochondrial genomes2002In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 89, no 4, p. 677-687Article in journal (Refereed)
    Abstract [en]

    Phylogenetic interrelationships in the enlarged order Ericales were investigated by jackknife analysis of a combination of DNA sequences from the plastid genes rbcLndhFatpB, and the mitochondrial genes atp1 and matR. Several well‐supported groups were identified, but neither a combination of all gene sequences nor any one alone fully resolved the relationships between all major clades in Ericales. All investigated families except Theaceae were found to be monophyletic. Four families, Marcgraviaceae, Balsaminaceae, Pellicieraceae, and Tetrameristaceae form a monophyletic group that is the sister of the remaining families. On the next higher level, Fouquieriaceae and Polemoniaceae form a clade that is sister to the majority of families that form a group with eight supported clades between which the interrelationships are unresolved: Theaceae‐Ternstroemioideae with FicalhoaSladenia, and Pentaphylacaceae; Theaceae‐Theoideae; Ebenaceae and Lissocarpaceae; Symplocaceae; Maesaceae, Theophrastaceae, Primulaceae, and Myrsinaceae; Styracaceae and Diapensiaceae; Lecythidaceae and Sapotaceae; Actinidiaceae, Roridulaceae, Sarraceniaceae, Clethraceae, Cyrillaceae, and Ericaceae.

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