15 research outputs found
Phylogenetic studies of cyanobacterial lichens
Phylogenetic studies of cyanobacterial lichens
Lichens are symbiotic assemblages between fungi (mycobiont) and green algae (phycobiont) or/and cyanobacteria (cyanobiont). Fossil records show that lichen-like symbioses occurred already 600 million years ago. Lichen symbiosis has since then become an important life strategy for the Fungi, particularly for species in the phylum Ascomycota as approximately 98% of the lichenized fungal species are ascomycetes. The taxonomy of lichen associations is based on the mycobiont.
We reconstructed, using DNA sequence data, hypotheses of phylogenetic relationships of lichen-forming fungi that include species associated with cyanobacteria. These hypotheses of phylogeny should form the basis for the taxonomy. They also allowed studies of the origin and the evolution of specific symbioses. Genetic diversity and phylogenetic relationships of symbiotic cyanobionts were also studied in order to examine selectivity of cyanobionts and mycobionts as well as possible co-evolution between partners involved in lichen associations.
The suggested circumscription of the family Stereocaulaceae to include Stereocaulon and Lepraria is supported. The recently described crustose Stereocaulon species seem to be correctly placed in the genus, although Stereocaulon traditionally included only fruticose species. The monospecific crustose genus Muhria is also shown to be best placed in Stereocaulon. Family Lobariaceae as currently delimited is monophyletic. Within Lobariaceae genus Sticta including Dendriscocaulon dendroides form a monophyletic group while the genera Lobaria and Pseudocyphellaria are non-monophyletic. A new classification of Lobariaceae is obviously needed. Further studies are however required before a final proposal for a new classification can be made.
Our results show that the cyanobacterial symbiotic state has been gained repeatedly in the Ascomycota while losses of symbiotic cyanobacteria appear to be rare. The symbiosis with green algae is confirmed to have been gained repeatedly in Ascomycota but also repeatedly lost. Cyanobacterial symbioses therefore seem to be more stable than green algal associations. Cyanobacteria are perhaps more beneficial for the lichen fungi and therefore maintained. The results indicate a dynamic association of the lichen symbiosis. This evolutionary instability will perhaps be important for the lichen fungi as the utilization of options will perhaps enable lichens to colonize new substrates and survive environmental changes. Some cyanobacterial lichen genera seem to be highly selective towards the cyanobiont while others form symbioses with a broad spectrum of cyanobacteria. No evidence of co-evolution between fungi and cyanobacteria in cyanolichens could be demonstrated.SlÀktskapsförhÄllanden hos cyanobakterie lavar
Lavar Àr komplexa helheter dÀr en svamp lever i symbios med en alg eller en cyanobakterie. Lavar dÀr alla tre komponenterna ingÄr Àr ocksÄ vanliga. Fossilfynd har visat att lavliknande symbioser förekom redan för 600 miljoner Är sedan. Sedan dess har lavsymbiosen blivit en viktig överlevnadsstrategi för mÄnga svampar, speciellt för sporsÀckssvamparna; uppskattningsvis 98% av alla lavbildande svampar tillhör denna grupp. I klassificeringssystem behandlas lavar som lavbildande svampar och ingÄr i svampsystematiken.
I mitt avhandlingsarbete har slĂ€ktskapsförhĂ„llanden inom vĂ€l definierade grupper av lavbildande svampar som ingĂ„r symbios med cyanobakterier studerats med hjĂ€lp av DNA sekvens data. Dessa slĂ€ktskapsförhĂ„llanden bör stĂ„ som grund för klassificeringen. De möjliggör Ă€ven studier av evolutionen av olika typer av symbioser. Ăven den genetiska mĂ„ngfalden hos cyanobakterier i lavsymbioser studerades för att dels utreda om svamparna Ă€r selektiva vid val av cyanobakterier och dels pĂ„visa en eventuell samevolution mellan organismerna som ingĂ„r i lavsymbioserna.
VÄra resultat visar att familjen Stereocaulaceae Àr en vÀl avgrÀnsad grupp om man inkluderar slÀkten Stereocaulon och Lepraria. Noggrannare studier av slÀktet Stereocaulon visar att slÀktet, förutom de buskformiga arterna som traditionellt ingÄtt, Àven omfattar skorpformiga arter. SlÀktet Muhria som bestÄr av en skorpformig art bör Àven inkluderas i Stereocaulon. Familjen Lobariaceae visade sig vara en annan vÀl avgrÀnsad grupp. Inom familjen bildar slÀktet Sticta en avgrÀnsad grupp medan slÀkterna Lobaria och Pseudocyphellaria inte bildar avgrÀnsade grupper. De morfologiska karaktÀrerna som traditionellt har anvÀnts för att skilja dessa slÀkten Àr dÀrför inte anvÀndbara. Resultaten innebÀr att en ny klassificering inom familjen Àr nödvÀndig, men detta krÀver dock ytterligare studier.
VÄra resultat visar ocksÄ att egenskapen att leva i symbios med cyanobakterier har utvecklats flera gÄnger hos sporsÀckssvamparna och att egenskapen sÀllan har förlorats. Studien bekrÀftar tidigare resultat att symbios mellan sporsÀckssvampar och grönalger har uppstÄtt flera gÄnger men Àven förlorats upprepade gÄnger. Symbiosen med cyanobakterier verkar dÀrmed vara mer stabil Àn den med grönalger och vittnar om att den kanske Àr mer fördelaktig för lavsvamparna. Resultaten indikerar att lavsymbioserna Àr dynamiska. Detta kan vara till fördel för lavsvamparna; möjligheten att utnyttja olika strategier ger dem möjlighet att kolonisera nya vÀxtplatser och överleva förÀndringar i levnadsmiljön. Vissa av lavsvamparna verkar vara specifika vid valet av cyanobakterie medan andra bildar symbios med ett brett spektrum av cyanobakterier. Inga bevis för samevolution mellan lavsvampar och cyanobakterier kunde pÄvisas
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A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the
kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two
protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available
sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently
recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, âCandelariomycetidaeâ). Maximum likelihood phylogenetic analyses on four
multigene datasets assembled using a cumulative supermatrix approach with a progressively higher
number of species and missing data (5-gene, 5 + 4-gene, 5 + 4 + 3-gene and 5 + 4 + 3 + 2-gene datasets)
show that the current classification includes non-monophyletic taxa at various ranks, which need to be
recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two
newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families
(Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes
inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered
here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated
with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A
revised schematic classification at the family level in the phylogenetic context of widely accepted and
newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with
an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which
sequences were available for all five targeted genes and ending with the addition of taxa for which only two
genes have been sequenced) revealed relatively stable relationships for many families and orders.
However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial
loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships),
potentially including the misplacements of several taxa. Future phylogenetic analyses should include
additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part
of this study, a new module (ââHyphaââ) of the freely available Mesquite software was developed to compare
and display the internodal support values derived from this cumulative supermatrix approach.Keywords: Classification, Multi-gene phylogeny, Lichenized fungi, Systematics, Cumulative supermatrix, Lecanoromycete
Phylogenetic relationships and evolution of photobiont associations in the Lobariaceae (Peltigerales, Lecanoromycetes, Ascomycota)
Phylogenetic relationships of the family Lobariaceae (Lecanoromycetes, Ascomycota) were reconstructed using direct optimization of nuclear ITS and LSU, and mitochondrial SSU rDNA sequences. Delimitations of the genera currently included in the family were investigated. Relationships of austral temperate taxa occurring in New Zealand, Australia and southern South America were studied in detail. Finally, we studied the evolution of the symbiotic associations found in the family which proved to be monophyletic. Sticta, with the exception of S. oroborealis, but including Dendriscocaulon dendroides, was found to be monophyletic while the genera Lobaria and Pseudocyphellaria turned out to be non-monophyletic. The status of Lobariella, and Lobarina as independent genera was not supported. Relationships of southern temperate Sticta species indicate a common Gondwanan ancestor. In rest of the family, species from the austral temperate zone group together with more widespread species. The ancestor of the Lobariaceae was associated with cyanobacteria. Green algal photobionts have subsequently been acquired repeatedly, but also repeatedly lost within the family. The acquisition of green algae has not resulted in a complete loss of the cyanobacterial photobiont. The cyanobacterial symbioses therefore seem to be more stable than those with green algae
Evolution of cyanobacterial symbioses in Ascomycota.
Two fifths of the species in Ascomycota are lichen-forming, of which 10% and 3-4% have cyanobacteria as the primary and secondary photobionts respectively. To study the evolution of cyanobacterial symbioses, the phylogenetic relationships within the Ascomycota have been reconstructed. Phylogenetic analyses were made using direct optimization of nuclear SSU and LSU rDNA sequences under the parsimony optimality criterion. Our results indicate repeated evolution of the mutualistic assemblages between fungi and cyanobacteria. The stability of the cyanobacterial symbioses and the effects of photobiont alteration on the evolution of ascomycetes are discussed, as is the taxonomy of some cyanobacterial lichen taxa, and some future perspectives on the evolution of these ecologically important assemblages
Lasioloma antillarum (Ascomycota: Pilocarpaceae), a new lichenized fungus from the Antilles, and the importance of posterior annotations of sequence data in public repositories
We describe the new lichenized fungus Lasioloma antillarum LĂŒcking, Högnabba & Sipman from the Netherlands Antilles. The new species is characterized by a corticolous growth habit, apothecia with shortly tomentose margins, and rather small (35â50 Ă 12â16 ”m), muriform ascospores in numbers of 2(â4) per ascus. The material had originally been identified as Calopadia phyllogena (MĂŒll. Arg.) VÄzda, with associated sequence data, but in phylogenetic analyses consistently fell outside the latter genus. Its revised identification as a species of Lasioloma is consistent with its phylogenetic position and underlines the necessity of posterior annotations in public sequence repositories, in order to correct previous identifications
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MaddisonDavidIntegrativeBiologyMultigenePhylogeneticSynthesis.pdf
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the
kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two
protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available
sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently
recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, âCandelariomycetidaeâ). Maximum likelihood phylogenetic analyses on four
multigene datasets assembled using a cumulative supermatrix approach with a progressively higher
number of species and missing data (5-gene, 5 + 4-gene, 5 + 4 + 3-gene and 5 + 4 + 3 + 2-gene datasets)
show that the current classification includes non-monophyletic taxa at various ranks, which need to be
recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two
newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families
(Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes
inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered
here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated
with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A
revised schematic classification at the family level in the phylogenetic context of widely accepted and
newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with
an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which
sequences were available for all five targeted genes and ending with the addition of taxa for which only two
genes have been sequenced) revealed relatively stable relationships for many families and orders.
However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial
loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships),
potentially including the misplacements of several taxa. Future phylogenetic analyses should include
additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part
of this study, a new module (ââHyphaââ) of the freely available Mesquite software was developed to compare
and display the internodal support values derived from this cumulative supermatrix approach.Keywords: Lichenized fungi, Multi-gene phylogeny, Classification, Systematics, Lecanoromycetes, Cumulative supermatrixKeywords: Lichenized fungi, Multi-gene phylogeny, Classification, Systematics, Lecanoromycetes, Cumulative supermatri
Recommended from our members
MaddisonDavidIntegrativeBiologyMultigenePhylogeneticSynthesis_SupplementaryMaterial.zip
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the
kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two
protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available
sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently
recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, âCandelariomycetidaeâ). Maximum likelihood phylogenetic analyses on four
multigene datasets assembled using a cumulative supermatrix approach with a progressively higher
number of species and missing data (5-gene, 5 + 4-gene, 5 + 4 + 3-gene and 5 + 4 + 3 + 2-gene datasets)
show that the current classification includes non-monophyletic taxa at various ranks, which need to be
recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two
newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families
(Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes
inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered
here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated
with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A
revised schematic classification at the family level in the phylogenetic context of widely accepted and
newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with
an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which
sequences were available for all five targeted genes and ending with the addition of taxa for which only two
genes have been sequenced) revealed relatively stable relationships for many families and orders.
However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial
loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships),
potentially including the misplacements of several taxa. Future phylogenetic analyses should include
additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part
of this study, a new module (ââHyphaââ) of the freely available Mesquite software was developed to compare
and display the internodal support values derived from this cumulative supermatrix approach.Keywords: Multi-gene phylogeny, Classification, Lecanoromycetes, Lichenized fungi, Cumulative supermatrix, SystematicsKeywords: Multi-gene phylogeny, Classification, Lecanoromycetes, Lichenized fungi, Cumulative supermatrix, Systematic
Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers
Fourteen genera belong to a monophyletic core of cetrarioid lichens, Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, Usnocetraria and Vulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, ÎČ-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the genera Allocetraria, Cetraria s. str., Cetrariella and Vulpicida. Arctocetraria, Cetreliopsis, Kaernefeltia and Tuckermanella are monophyletic genera, whereas Cetraria, Flavocetraria and Tuckermannopsis are polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known species Cetraria annae is analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy of Cetraria annae and Flavocetraria minuscula are also provided