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  • 151. Fuchs, Jerome
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Pasquet, Eric
    Mitochondrial phylogeographic structure of the white-browed piculet (Sasia ochracea): cryptic genetic differentiation and endemism in Indochina2008In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 35, no 3, p. 565-575Article in journal (Refereed)
  • 152. Fuchs, Jerome
    et al.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Pasquet, Eric
    Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae)2006In: Journal of Avian Biology, ISSN 0908-8857, E-ISSN 1600-048X, Vol. 37, no 5, p. 487-496Article in journal (Refereed)
  • 153. Fuchs, Jerome
    et al.
    Ohlson, Jan I
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Pasquet, Eric
    Synchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data2007In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 36, no 1, p. 11-25Article in journal (Refereed)
  • 154. Fuchs, Jérôme
    et al.
    Pons, Jean-Marc
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Bonillo, Céline
    Couloux, Arnaud
    Pasquet, Eric
    Molecular support for a rapid cladogenesis of the woodpecker clade Malarpicini, with further insights into the genus Picus (Piciformes: Picinae).2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 1, p. 34-46Article in journal (Refereed)
    Abstract [en]

    Previous studies have suggested that the woodpecker genus Picus (Aves: Picidae) may not be monophyletic. In order to evaluate this hypothesis, we analyzed DNA sequences from all but two species of Picus, as well as from representatives of all genera in the tribe Malarpicini, within which Picus is nested. We sequenced seven loci (four autosomal, one Z-linked and two mitochondrial) with different evolutionary dynamics. The species currently placed in Picus fall into two subclades that may not form a monophyletic assemblage. Consequently, we propose to place miniaceus Pennant 1769, flavinucha Gould 1834 and mentalis Temminck 1825 in the genus Chrysophlegma Gould, 1850, while the remaining species are retained in Picus. The inclusion in our study of representatives of all genera included in the tribe Malarpicini, a group of woodpeckers which has proven difficult to resolve in several previous molecular studies, also allowed us to determine the earliest divergences within this clade. The results suggest that the low level of basal resolution in Malarpicini is attributable to multiple cladogenetic events in a short period of time rather than insufficient character sampling. This conclusion is supported by the observation of nucleotide insertion-deletions that support mutually exclusive phylogenetic hypotheses in different gene trees. We attribute this pattern of incongruent indels, together with short internodes in the tree, to incomplete lineage sorting.

  • 155. Fuchs, Jérôme
    et al.
    Pons, Jean-Marc
    Liu, Liang
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Couloux, Arnaud
    Pasquet, Eric
    A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae).2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, no 3, p. 578-88Article in journal (Refereed)
    Abstract [en]

    The ever increasing number of analysed loci in phylogenetics has not only allowed resolution of some parts of the Tree of Life but has also highlighted parts of the tree where incongruent signals among loci were detected. Previous molecular studies suggested conflicting relationships for the New World genus Campephilus, being either associated to the Megapicini or Dendropocini. Yet, the limited number of analysed loci and the use of the concatenation approach to reconstruct the phylogeny prevented the disentanglement of lineage sorting and introgression as causal explanation of this topological conflict. We sequenced four mitochondrial, nine autosomal and three Z-linked loci and used a method that incorporates population level processes into the phylogenetic framework to understand which process (lineage sorting of genetic polymorphism or hybridization/introgression) best explains this conflict. Our analyses revealed that the autosomal FGB intron-7 and to a lesser extent the Z-linked loci have a different phylogenetic history from the mitochondrial loci and some other nuclear loci we analysed. We suggest that this conflicting pattern is the result of introgression consecutive to a hybridization event at the time when members of the Campephilus and melanerpine (Melanerpes and Sphyrapicus) lineages colonized the New World. The case of Campephilus highlights that the mitochondrial genome does not always carry the 'wrong' phylogenetic signal after a past hybridization event. Indeed, we here emphasise that the signature of such event can also be detected in the nuclear genome. With the ongoing increase in the number of loci analysed in phylogenetic studies, it is very likely that further cases will be discovered. Our current results indicate that (1) the genus Campephilus is related to the Asian genera Blythipicus, Chrysocolaptes and Reinwardtipicus, in accordance with morphological data and (2) that the nuclear genome of Campephilus is likely the mixture of two unrelated lineages. Yet, further work with a denser sampling of loci is necessary to evaluate the extant of the Sphyrapicus/Melanerpes lineage nuclear genome that introgressed into the Campephilus genome.

  • 156. Gargas, Andrea
    et al.
    DePriest, Paula T
    Grube, Martin
    Tehler, Anders
    Swedish Museum of Natural History, Department of Botany.
    Multiple origins of lichen symbiosis in fungi suggested by SSU rDNA phylogeny1995In: Science, Vol. 268, p. 1492-1495Article in journal (Refereed)
  • 157. Gaya, Ester
    et al.
    Fernández-Brime, Samantha
    Swedish Museum of Natural History, Department of Botany.
    Vargas, Reinaldo
    Lachlan, Robert F.
    Gueidan, Cécile
    Ramírez-Mejía, Martín
    Lutzoni, François
    The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 37, p. 11600-11605Article in journal (Refereed)
    Abstract [en]

    Adaptive radiations play key roles in the generation of biodiversity and biological novelty, and therefore understanding the factors that drive them remains one of the most important challenges of evolutionary biology. Although both intrinsic innovations and extrinsic ecological opportunities contribute to diversification bursts, few studies have looked at the synergistic effect of such factors. Here we investigate the Teloschistales (Ascomycota), a group of >1,000 lichenized species with variation in species richness and phenotypic traits that hinted at a potential adaptive radiation. We found evidence for a dramatic increase in diversification rate for one of four families within this order—Teloschistaceae—which occurred ∼100 Mya (Late Cretaceous) and was associated with a switch from bark to rock and from shady to sun-exposed habitats. This adaptation to sunny habitats is likely to have been enabled by a contemporaneous key novel phenotypic innovation: the production in both vegetative structure (thallus) and fruiting body (apothecia) of anthraquinones, secondary metabolites known to protect against UV light. We found that the two ecological factors (sun exposure and rock substrate) and the phenotypic innovation (anthraquinones in the thallus) were all significant when testing for state-dependent shifts in diversification rates, and together they seem likely to be responsible for the success of the Teloschistaceae, one of the largest lichen-forming fungal lineages. Our results support the idea that adaptive radiations are driven not by a single factor or key innovation, but require a serendipitous combination of both intrinsic biotic and extrinsic abiotic and ecological factors.

  • 158. Gaytan, Alvaro
    et al.
    Bergsten, Johannes
    Swedish Museum of Natural History, Department of Zoology.
    Canelo, Tara
    Pérez‐Izquierdo, Carlos
    Santoro, Maria
    Bonal, Raul
    DNA Barcoding and geographical scale effect: The problems of undersampling genetic diversity hotspots2020In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 10, p. 10754-10772Article in journal (Refereed)
    Abstract [en]

    DNA barcoding identification needs a good characterization of intraspecific genetic divergence to establish the limits between species. Yet, the number of barcodes per species is many times low and geographically restricted. A poor coverage of the species distribution range may hamper identification, especially when undersampled areas host genetically distinct lineages. If so, the genetic distance between some query sequences and reference barcodes may exceed the maximum intraspecific threshold for unequivocal species assignation. Taking a group of Quercus herbivores (moths) in Europe as model system, we found that the number of DNA barcodes from southern Europe is proportionally very low in the Barcoding of Life Data Systems. This geographical bias complicates the identification of southern query sequences, due to their high intraspecific genetic distance with respect to barcodes from higher latitudes. Pairwise intraspecific genetic divergence increased along with spatial distance, but was higher when at least one of the sampling sites was in southern Europe. Accordingly, GMYC (General Mixed Yule Coalescent) single-threshold model retrieved clusters constituted exclusively by Iberian haplotypes, some of which could correspond to cryptic species. The number of putative species retrieved was more reliable than that of multiple-threshold GMYC but very similar to results from ABGD and jMOTU. Our results support GMYC as a key resource for species delimitation within poorly inventoried biogeographic regions in Europe, where historical factors (e.g., glaciations) have promoted genetic diversity and singularity. Future European DNA barcoding initiatives should be preferentially performed along latitudinal gradients, with special focus on southern peninsulas. 

  • 159.
    Gelang, Magnus
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Cibois, Alice
    Pasquet, Eric
    Olsson, Urban
    Alstrom, Per
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification2009In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 38, no 3, p. 225-236Article in journal (Refereed)
  • 160. Gilbert, M Thomas P
    et al.
    Drautz, Daniela I
    Lesk, Arthur M
    Ho, Simon Y W
    Qi, Ji
    Ratan, Aakrosh
    Hsu, Chih-Hao
    Sher, Andrei
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Götherström, Anders
    Tomsho, Lynn P
    Rendulic, Snjezana
    Packard, Michael
    Campos, Paula F
    Kuznetsova, Tatyana V
    Shidlovskiy, Fyodor
    Tikhonov, Alexei
    Willerslev, Eske
    Iacumin, Paola
    Buigues, Bernard
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Germonpré, Mietje
    Kosintsev, Pavel
    Nikolaev, Vladimir
    Nowak-Kemp, Malgosia
    Knight, James R
    Irzyk, Gerard P
    Perbost, Clotilde S
    Fredrikson, Karin M
    Harkins, Timothy T
    Sheridan, Sharon
    Miller, Webb
    Schuster, Stephan C
    Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes.2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 24, p. 8327-32Article in journal (Refereed)
    Abstract [en]

    We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximately 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the (14)C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

  • 161. Grewe, F.
    et al.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Lumbsch, H. Thorsten
    Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)2020In: IMA Fungus, ISSN 2210-6340, E-ISSN 2210-6359, Vol. 11, article id 11: 27Article in journal (Refereed)
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  • 162. Grube, Martin
    et al.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Lichenized fungi and the evolution of symbiontic organization2018In: The Fungal Kingdom / [ed] Heitman, J., Howler, B.J., Crous, P.W., Stukenbrock, E.H., James, T.Y. and Gow, N.A.R., Washington DC: The American Society for Microbiology , 2018, p. 749-765Chapter in book (Refereed)
  • 163. Grube, Martin
    et al.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Lichenized fungi and the evolution of symbiotic organization.2016In: Microbiology Spectrum, E-ISSN 2165-0497, Vol. 4, no 6, article id FUNK-0011-2016Article in journal (Refereed)
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  • 164. Gustafson, Grey T.
    et al.
    Bergsten, Johannes
    Swedish Museum of Natural History, Department of Zoology.
    Randriamihaja, Jacquelin Herisahala
    Miller, Kelly
    University of New Mexico.
    The morphology and behavior of the endemic Malagasy whirligig beetle Heterogyrus milloti Legros, 1953 (Coleoptera: Gyrinidae: Heterogyrinae)2017In: The Coleopterists bulletin, ISSN 0010-065X, E-ISSN 1938-4394, Vol. 71, no 2, p. 315-328Article in journal (Refereed)
    Abstract [en]

    The Malagasy endemic whirligig beetle Heterogyrus milloti Legros, 1953 is redescribed. Jumping behavior of H. milloti is reported here for the first time with video recordings provided. Results of a behavioral experiment conducted in the field demonstrate H. milloti jumps in a targeted manner in a downstream direction. The unique habitat of H. milloti is described in detail with both image and video of the habitat included. Morphology of H. milloti is discussed in detail, revealing symplesiomorphies with Spanglerogyrus Folkerts, 1979, characters forming transitional series between Spanglerogyrus and the Gyrininae, and features unique to H. milloti. The potential adaptive significance of these peculiar morphological features in association with the habitat of H. milloti is discussed. Finally, an argument for the necessity of conservation of this species is made, and common names in English, French, Malagasy, and Swedish for H. milloti are proposed to aid conservation efforts.

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  • 165. Gustafson, Grey T.
    et al.
    Prokin, Alexander A.
    Bukontaite, Rasa
    Swedish Museum of Natural History, Department of Zoology. Stockholm University.
    Miller, Kelly
    University of New Mexico.
    Tip-dated phylogeny of whirligig beetles reveals ancient lineage surviving on Madagascar2017In: Scientific Reports, E-ISSN 2045-2322, Vol. 7, p. 1-9, article id 8619Article in journal (Refereed)
    Abstract [en]

    The temporal origin of Madagascar’s extraordinary endemic diversity is debated. A preference for Cenozoic dispersal origins has replaced the classical view of Mesozoic vicariance in the wake of molecular dating. However, evidence of ancient origins is mounting from arthropod groups. Using phylogenetic ‘tip-dating’ analysis with fossils, we show that a whirligig beetle species, Heterogyrus milloti, inhabiting forest streams in southeastern Madagascar is the last survivor of a once dominant and widespread Mesozoic group. With a Late Triassic to Early Jurassic origin (226–187 Ma) it is the hitherto oldest dated endemic lineage of animal or plant on Madagascar. Island biotas’ sensitivity to extinction is well known, but islands can also provide refuge from continental extinction. Heterogyrus milloti is an irreplaceable link to the freshwater biota of the Mesozoic and serves as a reminder of what may be lost without critical conservation e orts on Madagascar. 

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  • 166. Gutiérrez-Larruscain, David
    et al.
    Santos-Vicente, Maria
    Anderberg, Arne Alfred
    Swedish Museum of Natural History, Department of Botany.
    Rico, Enrique
    Montserrat Martinez-Ortega, Maria
    Phylogeny of the Inula group (Asteraceae: Inuleae): Evidence from nuclear and plastid genomes and a recircumscription of Pentanema2018In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 67, no 1, p. 149-164Article in journal (Refereed)
    Abstract [en]

    The Inula complex (Asteraceae: Inulinae) is a monophyletic group which comprises eight genera distributed in Eurasia and Africa: Amblyocarpum, Carpesium, Chrysophthalmum, Inula, Pentanema, Rhanteriopsis, Telekia, and Varthemia. With the aim to shed light on the circumscription of these genera, phylogenetic analyses were performed with 293 new DNA sequences (ITS region from nrDNA and three plastid spacers from cpDNA: rps16-trnQ, rpl32-trnL, ndhF-rpl32). It is concluded that both Inula and Pentanema are paraphyletic and that generic delimitations within the Inula complex need to be revised. Based on the results of the analyses, together with morphological and karyological data, we argue that the best solution is a new circumscription of the genus Pentanema including an amended description and 24 new combinations of former Inula species. Resurrection of the names Codonocephalum, Monactinocephalus and Vicoa is proposed to preserve the monophyly of the genera included in the Inula complex. Incongruences between nrDNA and cpDNA are documented and discussed.

  • 167.
    Hansen, Karen
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Olariaga, Ibai
    Swedish Museum of Natural History, Department of Botany.
    Species limits and relationships within Otidea inferred from multiple gene phylogenies2015In: Persoonia, ISSN 0031-5850, E-ISSN 1878-9080, Vol. 35, p. 148-165Article in journal (Refereed)
    Abstract [en]

    The genus Otidea is one of the more conspicuous members of the Pyronemataceae, with high speciesdiversity in hemiboreal and boreal forests. The genus is morphologically coherent and in previous higher-level multigeneanalyses it formed a highly supported monophyletic group. Species delimitation within Otidea is controversialand much confusion has prevailed in the naming of taxa. To provide a phylogenetic hypothesis of Otidea, elucidatespecies diversity and limits we compiled a four-gene dataset including the nuclear LSU rDNA and three nuclearprotein-coding genes (RPB1, RPB2 and EF-1α) for 89 specimens (total 4 877 nucleotides). These were selected froma larger sample of material studied using morphology and 146 ITS (ITS1-5.8S-ITS2) and 168 LSU rDNA sequencesto represent the full genetic diversity. Using genealogical concordance phylogenetic species recognition (GCPSR),Bayesian and maximum likelihood analyses of the individual datasets resolved 25 species of Otidea. An additionaleight singletons are considered to be distinct species, because they were genetically divergent from their sisters.Sequences of multiple genes were included from 13 holotypes, one neotype and three epitypes. Otidea angusta,O. myosotis and O. papillata f. pallidefurfuracea are nested within O. nannfeldtii, O. leporina and O. tuomikoskii,respectively and are considered synonyms. Otidea cantharella var. minor is shown to be a distinct species. Fivenew species were discovered: O. oregonensis and O. pseudoleporina for North America; and O. borealis, O. brunneoparvaand O. subformicarum for Europe. The analyses of the individual four gene datasets yielded phylogeniesthat were highly concordant topologically, except for the RPB1 that showed supported conflict for some nodes inBayesian analysis. Excluding the RPB1 from the combined analyses produced an identical topology to the four-genephylogeny, but with higher support for several basal nodes and lower support for several shallow nodes. We argueto use the three-gene dataset to retrieve the maximum support for the higher-level relationships in Otidea, but stillutilise the signal from the RPB1 for the delimitation and relationships of closely related species. From the four generegions utilised, EF-1α and RPB1 have the strongest species recognition power, and with higher amplification successEF-1α may serve as the best secondary barcoding locus for Otidea (with ITS being a primary). The phylogenyfrom the three- and four-gene datasets is fully resolved and strongly supported in all branches but one. Two majorclades, as part of six inclusive clades A–F, are identified – and ten subclades within these: A) O. platyspora andO. alutacea subclades, and B) O. papillata, O. leporina, O. tuomikoskii, O. cantharella, O. formicarum, O. unicisa,O. bufonia-onotica and O. concinna subclades. Morphological features in Otidea appear to be fast evolving andprone to shifts, and are poor indicators of higher-level relationships. Nevertheless, a conspicuous spore ornament isa synapomorphy for the O. unicisa subclade (/Otideopsis); all other species in Otidea have smooth or verruculose (inSEM) spores. Exclusively pale to bright yellow apothecia and straight to curved, broadly clavate to distinctly capitateparaphyses are synapomorphies for a restricted O. concinna subclade (/Flavoscypha). The curved to hooked apicesof the paraphyses is suggested to be a symplesiomorphic trait for the genus. The reaction of resinous exudateson the outermost excipular cells that coalesce into amber drops in Melzer’s reagent is likely an ancestral state forclade B. We estimate that Otidea consists of 47 species worldwide, based on all available information (includingmorphology, ITS or LSU sequences, and literature descriptions). Three fifths of the species occur in Europe, with20 species recognised as endemic. At least 14 species occur in North America and 17 in Asia, with eight and tenspecies considered endemic to each continent, respectively. Our knowledge about Otidea in Asia is still fragmentaryand the diversity likely much higher.

  • 168.
    Hansen, Karen
    et al.
    Swedish Museum of Natural History, Department of Botany. Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
    Perry, Brian A.
    Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
    Dranginis, Andrew W.
    Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
    Pfister, Donald H.
    Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA 02138, USA.
    A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected lifehistory traits2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 67, p. 311-335Article in journal (Refereed)
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  • 169.
    Hansen, Karen
    et al.
    Swedish Museum of Natural History, Department of Botany.
    S. Weber, Nancy
    Oregon State University, Department of Forest Ecosystems and Society, 321 Richardson Hall, Corvallis, OR 97331, USA.
    Landvik, Sara
    Novozymes A/S, Department of Fungal Screening, Smørmosevej 25, DK-2880 Bagsværd, Denmark.
    Phylogenetic relationships and distribution of Karstenella (Pezizomycetes)2008In: Karstenia, ISSN 0453-3402, Vol. 48, p. 13-19Article in journal (Refereed)
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  • 170.
    Hansen, Karen
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Schumacher, Trond
    Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway..
    Skrede, Inger
    Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway..
    Huhtinen, Seppo
    Herbarium, Biodiversity Unit, University of Turku, FI-20014 Turku, Finland..
    Wang, Xianghua
    Swedish Museum of Natural History, Department of Botany. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China..
    Pindara revisited – evolution and generic limits in Helvellaceae: Generic limits in Helvellaceae2019In: Persoonia, ISSN 0031-5850, E-ISSN 1878-9080, Vol. 42, p. 186-204Article in journal (Refereed)
    Abstract [en]

    The Helvellaceae encompasses taxa that produce some of the most elaborate apothecial forms, as well as hypogeous ascomata, in the class Pezizomycetes (Ascomycota). While the circumscription of the Helvellaceae is clarified, evolutionary relationships and generic limits within the family are debatable. A robust phylogeny of the Helvellaceae, using an increased number of molecular characters from the LSU rDNA, RPB2 and EF-1α gene regions (4 299 bp) and a wide representative sampling, is presented here. Helvella s.lat. was shown to be polyphyletic, because Helvella aestivalis formed a distant monophyletic group with hypogeous species of Balsamia and Barssia. All other species of Helvella formed a large group with the enigmatic Pindara (/Helvella) terrestris nested within it. The ear-shaped Wynnella constitutes an independent lineage and is recognised with the earlier name Midotis. The clade of the hypogeous Balsamia and Barssia, and H. aestivalis is coherent in the three-gene phylogeny, and considering the lack of phenotypic characters to distinguish Barssia from Balsamia we combine species of Barssia, along with H. aestivalis, in Balsamia. The closed/tuberiform, sparassoid H. astieri is shown to be a synonym of H. lactea; it is merely an incidental folded form of the saddle-shaped H. lactea. Pindara is a sister group to a restricted Helvella, i.e., excluding the /leucomelaena lineage, on a notably long branch. We recognise Pindara as a separate genus and erect a new genus Dissingia for the /leucomelaena lineage, viz. H. confusa, H. crassitunicata, H. leucomelaena and H. oblongispora. Dissingia is supported by asci that arise from simple septa; all other species of Helvellaceae have asci that arise from croziers, with one exception being the /alpina-corium lineage of Helvella s.str. This suggests ascus development from croziers is the ancestral state for the Helvellaceae and that ascus development from simple septa has evolved at least twice in the family. Our phylogeny does not determine the evolutionary relationships within Helvella s.str., but it is most parsimonious to infer that the ancestor of the helvelloids produced subsessile or shortly stipitate, cup-shaped apothecia. This shape has been maintained in some lineages of Helvella s.str. The type species of Underwoodia, Underwoodia columnaris, is a sister lineage to the rest of the Helvellaceae

  • 171.
    Hartop, Emily
    et al.
    Department of Zoology Stockholm University Stockholm Sweden;Station Linné Färjestaden Sweden.
    Häggqvist, Sibylle
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Ulefors, Sven Olof
    Färgerivägen 9 Alsterbro Sweden.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Scuttling towards monophyly: phylogeny of the mega‐diverse genus Megaselia (Diptera: Phoridae)2020In: Systematic Entomology, ISSN 0307-6970, E-ISSN 1365-3113, Vol. 46, no 1, p. 71-82Article in journal (Refereed)
  • 172.
    Hartop, Emily
    et al.
    Department of Zoology, Stockholm University , Frescativägen, 114 19 Stockholm, Sweden;Station Linné , Skogsby 161, 386 93 Färjestaden, Sweden;Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science , Museum für Naturkunde, Invalidenstraße 43, 10115 Berlin, Germany.
    Srivathsan, Amrita
    Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science , Museum für Naturkunde, Invalidenstraße 43, 10115 Berlin, Germany;Department of Biological Sciences, National University of Singapore , 21 Lower Kent Ridge Rd., Singapore 119077, Singapore.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Meier, Rudolf
    Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science , Museum für Naturkunde, Invalidenstraße 43, 10115 Berlin, Germany;Department of Biological Sciences, National University of Singapore , 21 Lower Kent Ridge Rd., Singapore 119077, Singapore.
    Towards Large-Scale Integrative Taxonomy (LIT): Resolving the Data Conundrum for Dark Taxa2022In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 71, no 6, p. 1404-1422Article in journal (Refereed)
  • 173. Haussler, David
    et al.
    O'Brien, Stephen J.
    Ryder, Oliver A.
    Barker, F. Keith
    Clamp, Michele
    Crawford, Andrew J.
    Hanner, Robert
    Hanotte, Olivier
    Johnson, Warren E.
    McGuire, Jimmy A.
    Miller, Webb
    Murphy, Robert W.
    Murphy, William J.
    Sheldon, Frederick H.
    Sinervo, Barry
    Venkatesh, Byrappa
    Wiley, Edward O.
    Allendorf, Fred W.
    Amato, George
    Baker, C. Scott
    Bauer, Aaron
    Beja-Pereira, Albano
    Bermingham, Eldredge
    Bernardi, Giacomo
    Bonvicino, Cibele R.
    Brenner, Sydney
    Burke, Terry
    Cracraft, Joel
    Diekhans, Mark
    Edwards, Scott
    Ericson, Per G. P.
    Estes, James
    Fjelsda, Jon
    Flesness, Nate
    Gamble, Tony
    Gaubert, Philippe
    Graphodatsky, Alexander S.
    Graves, Jennifer A. Marshall
    Green, Eric D.
    Green, Richard E.
    Hackett, Shannon
    Hebert, Paul
    Helgen, Kristofer M.
    Joseph, Leo
    Kessing, Bailey
    Kingsley, David M.
    Lewin, Harris A.
    Luikart, Gordon
    Martelli, Paolo
    Moreira, Miguel A. M.
    Nguyen, Ngan
    Orti, Guillermo
    Pike, Brian L.
    Rawson, David Michael
    Schuster, Stephan C.
    Seuanez, Hector N.
    Shaffer, H. Bradley
    Springer, Mark S.
    Stuart, Joshua Michael
    Sumner, Joanna
    Teeling, Emma
    Vrijenhoek, Robert C.
    Ward, Robert D.
    Warren, Wesley C.
    Wayne, Robert
    Williams, Terrie M.
    Wolfe, Nathan D.
    Zhang, Ya-Ping
    Graph-Odatsky, Alexander
    Johnson, Warren E.
    Felsenfeld, Adam
    Turner, Steve
    Genome, K. Community Scientists
    Mammals, Grp
    Birds, Grp
    Amphibians Reptiles, Grp
    Fishes, Grp
    General Policy, Grp
    Anal, Grp
    Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species2009In: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 100, no 6, p. 659-674Article in journal (Other academic)
  • 174. Havran, J. Christopher
    et al.
    Nylinder, Stephan
    Swenson, Ulf
    Swedish Museum of Natural History, Department of Botany.
    Taxonomic Reevaluation of Endemic Hawaiian Planchonella (Sapotaceae)2021In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 46, p. 875-888Article in journal (Refereed)
    Abstract [en]

    Planchonella (Sapotaceae) in Hawaii has a complicated taxonomic history that has resulted in considerable confusion among bota- nists and conservation practitioners. Up to seven different species and several varieties have been described in Hawaii, with the most recent taxonomic evaluation recognizing one species, P. sandwicensis. We have conducted a phylogenetic study of Hawaiian Planchonella using molec- ular (ETS, ITS, and RPB2) and morphological data to infer whether one or several species can be distinguished. In line with earlier research based on molecular data, we find that Planchonella in Hawaii is comprised of two well-supported clades distinguished by fruit color: yellow or purple. The purple-fruited clade contains individuals with flat leaf blades, long pedicels, and greenish corollas, a species corresponding to P. sandwicensis, distributed on all Hawaiian Islands except the island of Hawaii. The yellow-fruited clade possesses leaves that are frequently longitudinally rolled, wavy or distally deflexed, short pedicels, and yellow or cream (rarely greenish) corollas, a species corresponding to P. spathulata that is distributed on all Hawaiian Islands but is believed rare in Kauai. Both species can set fruit with aborted ovules, resulting in small fruits that look dissimilar to well-developed fruit. The species can occur in sympatry, where P. sandwicensis seems to be better adapted to slightly wetter forests and higher altitudes, whereas P. spathulata usually occurs at lower elevations in mesic to dry forests. Both species exhibit large morphological variation and overlap, resulting in many previous collections with inadequate label information, which has impeded correct taxonomic determinations. We refrain from recognizing infraspecific taxa because there is no morphological coherence, no molecular support, and it is unhelpful for species conservation. Five lectotypes are here designated. Both species are assessed for conservation status according to IUCN guidelines and are tentatively proposed as species of Least Concern.

  • 175. Hawksworth, D.L.
    et al.
    Millanes, A.M.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Fixing the application of the generic name Naematelia (Tremellales) by lectotypification.2016In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 65, p. 1093-1096Article in journal (Refereed)
    Download full text (pdf)
    fulltext
  • 176. He, Mao-Qiang
    et al.
    Zhao, Rui-Lin
    Liu, Dong-Mei
    Denchev, Teodor T.
    Begerow, Dominik
    Yurkov, Andrey
    Kemler, Martin
    Millanes, Ana M.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    McTaggart, A. R.
    Shivas, Roger G.
    Buyck, Bart
    Chen, Jie
    Vizzini, Alfredo
    Papp, Viktor
    Zmitrovich, Ivan V.
    Davoodian, Naveed
    Hyde, Kevin D.
    Species diversity of Basidiomycota2022In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 114, no 1, p. 281-325Article in journal (Refereed)
    Download full text (pdf)
    fulltext
  • 177. Healy, Rosanne
    et al.
    Pfister, Donald H.
    Rossman, Amy
    Marvanová, L.
    Hansen, Karen
    Swedish Museum of Natural History, Department of Botany.
    Competing sexual-asexual generic names of Pezizomycetes and recommendations for use.2016In: IMA Fungus, ISSN 2210-6340, E-ISSN 2210-6359, Vol. 7, no 2, p. 285-288Article in journal (Refereed)
    Abstract [en]

    Following the change that eliminated dual naming of sexual and asexual morphs of fungi, generic names of Pezizomycetes have been evaluated to determine which of the competing names should be recommended for use. Evaluation is based on congruence of type species to determine if the names are congeneric and which name is most commonly cited as well as priority. In the Pezizomycetes six pairs of generic names were determined to compete. In all cases the older name, representing the sexual morph, is recommended for use, specifically Caloscypha rather than Geniculodendron, Desmazierella rather than Verticicladium, Miladina rather than Actinosporella, Morchella rather than Costantinella, Sarcoscypha rather than Molliardiomyces, and Trichophaea rather than Dichobotrys. 

  • 178.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Amblystegiaceae (introduction and keys), Cratoneuron, Palustriella, Platydictya (H. A. Crum & L. Hedenäs), Campyliadelphus, Campylium, Drepanocladus, Pseudocalliergon, Sanionia, Conardia (H. A. Crum & L. Hedenäs), Campylophyllum, Calliergonaceae (whole family)2014In: Flora of North America, north of Mexico. Volume 28. Bryophyta, Part 2 / [ed] Flora of North America Editorial Committee, New York, Oxford: Oxford University Press, 2014Chapter in book (Refereed)
  • 179.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Brachythecium tauriscorum Molendo, a widely distributed Arctic-alpine species2017In: Journal of Bryology, ISSN 0373-6687, E-ISSN 1743-2820Article in journal (Refereed)
  • 180.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Conservation status of the two cryptic species of Hamatocaulis vernicosus (Bryophyta) inSweden2018In: Journal of Bryology, ISSN 0373-6687, E-ISSN 1743-2820, Vol. 40, no 4, p. 307-315Article in journal (Refereed)
  • 181.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Cryptic and morphologically recognizable species diversity within Scandinavian Plagiopus oederianus (Bryophyta: Bartramiaceae)2020In: Lindbergia, ISSN 0105-0761, E-ISSN 2001-5909, Vol. 43, p. 1-12, article id linbg.01130Article in journal (Refereed)
  • 182.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    DisentanglingScandinavian species hidden within Meesia uliginosa Hedw. s.l. (Bryophyta, Meesiaceae)2020In: Lindbergia, ISSN 0105-0761, E-ISSN 2001-5909, Vol. 42, p. 1-15, article id linbg.01125Article in journal (Refereed)
  • 183.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Forskning avslöjar dold mångfald och nya arter bland mossor i norr2020In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 114, p. 254-259Article in journal (Other (popular science, discussion, etc.))
  • 184.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Incipient speciation in Scandinavian Distichium capillaceum (Distichiaceae, Bryophyta)2021In: Lindbergia, ISSN 0105-0761, E-ISSN 2001-5909, Vol. 42, p. 1-12, article id linbg.01144Article in journal (Refereed)
  • 185.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Intraspecific diversity matters in bryophyte conservation – ITS and rpl16 variation in European mosses2016In: Journal of Bryology, ISSN 0373-6687, E-ISSN 1743-2820, Vol. 38, p. 173-182Article in journal (Refereed)
  • 186.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Intraspecific genetic variation in selected mosses of Scandinavian interglacial refugia suggests contrasting distribution history patterns2014In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 176, p. 295-310Article in journal (Refereed)
  • 187.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Molecular andmorphological incongruence among the genera around Sarmentypnum (Bryophyta: Calliergonaceae)2015In: Nova Hedwigia: Zeitschrift für Kryptogamenkunde, ISSN 0029-5035, Vol. 100, p. 279-292Article in journal (Refereed)
  • 188.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Oncophorus demetrii, a fifth Scandinavian species of Oncophorus (Musci) possible to recognize by morphology2018In: Lindbergia, ISSN 0105-0761, E-ISSN 2001-5909, Vol. 41, p. 1-9, article id linbg.01098Article in journal (Refereed)
  • 189.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Oxyrrhynchium hians (Brachytheciaceae, Bryophyta) includes several morphologically distinct and cryptic species in northwestern Europe2024In: Lindbergia, ISSN 0105-0761, E-ISSN 2001-5909, Vol. 2024, article id e025731Article in journal (Refereed)
  • 190.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Phylogeographical patterns in the northwestern European moss Scorpidium revolvens (Sw. ex Anonymo) Rubers (Scorpidiaceae, Bryophyta)2024In: Journal of Bryology, ISSN 0373-6687, E-ISSN 1743-2820Article in journal (Refereed)
  • 191.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Potentially misleading phylogenetic signal and its explanation in single species studies – contrasting Loeskypnum badium, Sarmentypnum exannulatum and Warnstorfia fluitans2022In: The Bryologist, ISSN 0007-2745, E-ISSN 1938-4378, Vol. 125, p. 102-114Article in journal (Refereed)
  • 192.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Rhytidium rugosum (Bryophyta) colonized Scandinaviafrom at least two glacial refugial source populations2015In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, no 179, p. 635-657Article in journal (Refereed)
  • 193.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Scandinavian Oncophorus (Bryopsida, Oncophoraceae): species, cryptic species, and intraspecific variation2017In: European journal of taxonomy, E-ISSN 2118-9773, p. 1-34, article id 315Article in journal (Refereed)
  • 194.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Styv kalkmossa och andra kalkmossor i Sverige2015In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 109, p. 94-104Article in journal (Other (popular science, discussion, etc.))
  • 195.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Three molecular markers suggest different relationships among three Drepanocladus species (Bryophyta: Amblystegiaceae)2017In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 303, p. 521-529Article in journal (Refereed)
  • 196.
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Tortella rigens (Bryophyta, Pottiaceae): relationships, regional variation, and conservation aspects2015In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110Article in journal (Refereed)
  • 197.
    Hedenäs, Lars
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Bisang, Irene
    Swedish Museum of Natural History, Department of Botany.
    Infraspecific diversity in a spore-dispersed species with limited distribution range2015In: Systematics and Biodiversity, ISSN 1477-2000, E-ISSN 1478-0933, Vol. 13, p. 17-27Article in journal (Refereed)
  • 198.
    Hedenäs, Lars
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Collart, Flavien
    Heras, Patxi
    Infante, Marta
    Kooijman, Annemieke M.
    Kučera, Jan
    Distributions and habitats of the two partly allopatric cryptic species of the vulnerable moss Hamatocaulis vernicosus (Bryophyta) in Europe2022In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339Article in journal (Refereed)
  • 199.
    Hedenäs, Lars
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Désamoré, A.
    Laenen, Benjamin
    Papp, Beata
    Quandt, Dietmar
    González-Mancebo, J. M.
    Patiño, Jairo
    Vanderpoorten, Alain
    Stech, Michael
    Three species for theprice of one within the moss Homalotheciumsericeum s.l.2014In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 63, p. 249-257Article in journal (Refereed)
  • 200.
    Hedenäs, Lars
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Heinrichs, Jochen
    Gallego, María Teresa
    The Scandinavian Syntrichia ruralis complex (Musci, Pottiaceae): a chaos of diversification2019In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 305, p. 639-661Article in journal (Refereed)
1234567 151 - 200 of 559
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