Aim: We have studied population genetic change through time in the Northern dragonhead, Dracoceph... more Aim: We have studied population genetic change through time in the Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae); a plant species that has experienced a drastic population decline and habitat loss in Europe. We aimed at adding a historic level to the monitoring of dragonhead by testing a microfluidic SNP array approach on herbarium specimens up to 200 years old and comparing the genomic results with that of modern populations in Norway. We also aimed to gain a more holistic species knowledge to guide monitoring efforts by combining herbarium genomics with ecological niche modelling (ENM). Location: Europe (mainly Norway) Methods: We have applied a microfluidic array consisting of 96 SNP markers on 130 herbarium specimens collected from 1820 to 2008. Obtained genotype data were compared with SNP data from modern samples using various population genetic analyses. We used sample metadata and observational records to model the species’ environmental niche. Results: The SNP a...
Additional file 4: Figure S2. Phylograms inferred from ML analysis of concatenated nucleotide seq... more Additional file 4: Figure S2. Phylograms inferred from ML analysis of concatenated nucleotide sequences of 79 protein-coding genes (dataset CR). A, phylogram showing branch lengths, where tips names are absent follow the same order as shown in B. Scale bar represents the mean number of nucleotide substitutions per site. B, maximum likelihood bootstrap support values and Bayesian inference posterior probabilities are shown above and below the branches, respectively.
Interesting lichenized and lichenicolous fungi found during the Nordic Lichen Society excursion i... more Interesting lichenized and lichenicolous fungi found during the Nordic Lichen Society excursion in Nord-Trondelag, Norway 2015
Sister group relations of Ethiopian species of Anthericum and Chlorophytum and variation patterns... more Sister group relations of Ethiopian species of Anthericum and Chlorophytum and variation patterns in the C. gallabatense and C. comosum complexes were studied using molecular phylogenetic analyses, morphometrics, and scanning electron microscopy of seed surfaces. Results indicate that molecular data largely support previous morphological conclusions, and that speciation has occurred in Ethiopia at least three times in Anthericum and repeatedly within different subclades of Chlorophytum. Areas particularly rich in endemic species are the lowland area around Bale Mountains in SE Ethiopia and in the Beninshangul Gumuz regional state in W Ethiopia near the border to Sudan. A new species, Chlorophytum mamillatum Elden & Nordal, is described, and the names C. tordense and C. tetraphyllum are re-instated.
A list of 120 taxa observed at the Vadstena Monastery churchyard includes some rare species and a... more A list of 120 taxa observed at the Vadstena Monastery churchyard includes some rare species and a few lichenicolous fungi. Lecanora semipallida is reported from the province Östergötland [Ostrogothia] for the first time.
Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe ... more Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL-trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. W...
ABSTRACT AimThe rare lichen species Staurolemma omphalarioides is known mainly from the lowlands ... more ABSTRACT AimThe rare lichen species Staurolemma omphalarioides is known mainly from the lowlands and coastal areas of the Mediterranean region but has also been found in coastal parts of central Norway. Despite extensive search efforts by experts for more than half a century, the species has been found nowhere in the gap. Our aim is to identify the most plausible explanation for this anomalous distribution by combining genetic analysis of archived specimens with distribution modelling.LocationEurope, western Middle East and North Africa (but mainly the Mediterranean and Atlantic floristic regions).Methods We used multi-locus DNA sequencing of archived specimens and phylogenetic and network analyses to reveal potential genetic lineages within S. omphalarioides. We used georeferenced specimens and bioclimatic variables to model the distributions of the species and two genetic lineages, and to find the main environmental correlates of the distributions.ResultsOur phylogeographical results show that S. omphalarioides contains genetic variation that correlates with geographical distance, although with a few shared haplotypes across disjunct ranges. Distributions of the species as well as the two genetic lineages are non-random. Distribution models predict occurrences of the species as well as one of its genetic lineages outside the current range of the species.Main conclusionsOur results indicate that neither the species nor its component genetic lineages have reached their potential distributions. Shared haplotypes across disjunct distributions, and absence from regions with suitable refugial habitats along the Atlantic coast of Western Europe, support long-distance dispersal, rather than vicariance, as the primary cause for the current distribution of the species.
Great care was taken to limit the possibility of host plant or other contamination of the parasit... more Great care was taken to limit the possibility of host plant or other contamination of the parasitic plant DNA samples, including careful dissection of tissues distal to the host-parasite interface. Measurements of floral diameters were obtained from published studies [1, 2] or from mature specimens of R. cantleyi, R. kerrii, R. pricei, and R. keithii (n = 45 in total). Gene Sampling Prior to using mitochondrial (mt) DNA to estimate relationships within Rafflesiaceae, we attempted to ensure that none of the genic regions we isolated were historically horizontally transferred after the origin of the family [3, 4]. To do this, we first performed a preliminary phylogenetic analysis with representatives of all currently recognized monophyletic rosid orders, as well as 2 members of Vitaceae, including the host plant of Rafflesia pricei (Tetrastigma diepenhorstii) so they could be directly compared. For all three mt genes (matR, atp6, and nad1B-C) Rafflesia, Rhizanthes, and Sapria were closely related to each other, and for matR and atp6, the three genera were estimated as members of Malpighiales, as expected [5, 6] (data not shown) suggesting
Fuscopannaria confusa is a rare lichen restricted to very humid localities in boreal forests. Two... more Fuscopannaria confusa is a rare lichen restricted to very humid localities in boreal forests. Two Fuscopannaria species, F. ahlneri and F. mediterranea, and Parmeliella parvula are morphologically problematic to distinguish from F. confusa. Our aim with the present study was to evaluate the taxonomic status of F. confusa and thereby clarify its conservation status in Norway. By phylogenetic analysis of multi-locus DNA sequences, we show that F. confusa is genetically well distinguished from F. ahlneri,F. mediterranea, and P. parvula. Fuscopannaria confusa should therefore be treated as a separate species. A species distribution modelling analysis indicates that F. confusa has a slightly continental but potentially wide geographic distribution in Norway. However, suitable localities are continuously being destroyed by clear-cut logging and hydroelectric power development. Because of the decline in suitable habitats, F. confusa should be regarded as highly threatened in Norway and lis...
ABSTRACT We have addressed phylogenetic relationships and tested hypotheses about five presumed s... more ABSTRACT We have addressed phylogenetic relationships and tested hypotheses about five presumed subgroups among 15 species of Hypocenomyce s.l. (including Pycnora) by use of nuclear (ITS, LSU) and mitochondrial (SSU) ribosomal DNA-regions. Bayesian, likelihood and parsimony phylogenetic analyses, of a dataset with broad Lecanoromycete taxon sampling, mostly support the five presumed subgroups, but two of these were found to be polyphyletic (the H. friesii-group and Pycnora). The seven supported Hypocenomyce s.l. clades belong in different genera, families, orders and even subclasses, and represent a remarkable example of morphological and ecological convergence. Based on our molecular phylogenetic results, we split Hypocenomyce into four genera placed in two subclasses: (1) Carbonicola gen. nov. (Carbonicolaceae fam. nov., Lecanorales, Lecanoromycetidae; including C. anthracophila comb. nov., C. foveata comb. nov., and C. myrmecina comb. nov.); (2) Fulgidea gen. nov. (Umbilicariaceae, Umbilicariales, Umbilicariomycetidae subcl. nov.; including F. oligospora comb. nov. and F. sierrae comb. nov.); (3) Hypocenomyce (Ophioparmaceae, Umbilicariales; including H. australis, H. scalaris, and H. tinderryensis; and (4) Xylopsora gen. nov. (Umbilicariaceae; including X. caradocensis comb. nov. and X. friesii comb. nov.). We split Pycnora into two genera: (1) Pycnora (Pycnoraceae fam. nov., Candelariales, “Candelariomycetidae”; including P. praestabilis, P. sorophora, and P. xanthococca); and (2) Toensbergia gen. nov. (Sporastatiaceae fam. nov., unknown order, ecanoromycetidae; including T. leucococca comb. nov.). We place Hypocenomyce isidiosa in Xylographa (Trapeliaceae, Baeomycetales, Ostropomycetidae; X. isidiosa comb. nov.). We place the Family Ophioparmaceae in the Umbilicariales. Our type studies have shown that the epithet “myrmecina” should replace “castaneocinerea”, and lectotypes are chosen for Lecidea friesii Ach., L. scalaris var. myrmecina Ach., Psora cladonioides var. albocervina Räsänen, and P. cladonioides var. castaneocinerea Räsänen. Elixia cretica is reported as new to North America (from Mexico) and Australia.
Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to... more Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry…
Aim: We have studied population genetic change through time in the Northern dragonhead, Dracoceph... more Aim: We have studied population genetic change through time in the Northern dragonhead, Dracocephalum ruyschiana (Lamiaceae); a plant species that has experienced a drastic population decline and habitat loss in Europe. We aimed at adding a historic level to the monitoring of dragonhead by testing a microfluidic SNP array approach on herbarium specimens up to 200 years old and comparing the genomic results with that of modern populations in Norway. We also aimed to gain a more holistic species knowledge to guide monitoring efforts by combining herbarium genomics with ecological niche modelling (ENM). Location: Europe (mainly Norway) Methods: We have applied a microfluidic array consisting of 96 SNP markers on 130 herbarium specimens collected from 1820 to 2008. Obtained genotype data were compared with SNP data from modern samples using various population genetic analyses. We used sample metadata and observational records to model the species’ environmental niche. Results: The SNP a...
Additional file 4: Figure S2. Phylograms inferred from ML analysis of concatenated nucleotide seq... more Additional file 4: Figure S2. Phylograms inferred from ML analysis of concatenated nucleotide sequences of 79 protein-coding genes (dataset CR). A, phylogram showing branch lengths, where tips names are absent follow the same order as shown in B. Scale bar represents the mean number of nucleotide substitutions per site. B, maximum likelihood bootstrap support values and Bayesian inference posterior probabilities are shown above and below the branches, respectively.
Interesting lichenized and lichenicolous fungi found during the Nordic Lichen Society excursion i... more Interesting lichenized and lichenicolous fungi found during the Nordic Lichen Society excursion in Nord-Trondelag, Norway 2015
Sister group relations of Ethiopian species of Anthericum and Chlorophytum and variation patterns... more Sister group relations of Ethiopian species of Anthericum and Chlorophytum and variation patterns in the C. gallabatense and C. comosum complexes were studied using molecular phylogenetic analyses, morphometrics, and scanning electron microscopy of seed surfaces. Results indicate that molecular data largely support previous morphological conclusions, and that speciation has occurred in Ethiopia at least three times in Anthericum and repeatedly within different subclades of Chlorophytum. Areas particularly rich in endemic species are the lowland area around Bale Mountains in SE Ethiopia and in the Beninshangul Gumuz regional state in W Ethiopia near the border to Sudan. A new species, Chlorophytum mamillatum Elden & Nordal, is described, and the names C. tordense and C. tetraphyllum are re-instated.
A list of 120 taxa observed at the Vadstena Monastery churchyard includes some rare species and a... more A list of 120 taxa observed at the Vadstena Monastery churchyard includes some rare species and a few lichenicolous fungi. Lecanora semipallida is reported from the province Östergötland [Ostrogothia] for the first time.
Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe ... more Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL-trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. W...
ABSTRACT AimThe rare lichen species Staurolemma omphalarioides is known mainly from the lowlands ... more ABSTRACT AimThe rare lichen species Staurolemma omphalarioides is known mainly from the lowlands and coastal areas of the Mediterranean region but has also been found in coastal parts of central Norway. Despite extensive search efforts by experts for more than half a century, the species has been found nowhere in the gap. Our aim is to identify the most plausible explanation for this anomalous distribution by combining genetic analysis of archived specimens with distribution modelling.LocationEurope, western Middle East and North Africa (but mainly the Mediterranean and Atlantic floristic regions).Methods We used multi-locus DNA sequencing of archived specimens and phylogenetic and network analyses to reveal potential genetic lineages within S. omphalarioides. We used georeferenced specimens and bioclimatic variables to model the distributions of the species and two genetic lineages, and to find the main environmental correlates of the distributions.ResultsOur phylogeographical results show that S. omphalarioides contains genetic variation that correlates with geographical distance, although with a few shared haplotypes across disjunct ranges. Distributions of the species as well as the two genetic lineages are non-random. Distribution models predict occurrences of the species as well as one of its genetic lineages outside the current range of the species.Main conclusionsOur results indicate that neither the species nor its component genetic lineages have reached their potential distributions. Shared haplotypes across disjunct distributions, and absence from regions with suitable refugial habitats along the Atlantic coast of Western Europe, support long-distance dispersal, rather than vicariance, as the primary cause for the current distribution of the species.
Great care was taken to limit the possibility of host plant or other contamination of the parasit... more Great care was taken to limit the possibility of host plant or other contamination of the parasitic plant DNA samples, including careful dissection of tissues distal to the host-parasite interface. Measurements of floral diameters were obtained from published studies [1, 2] or from mature specimens of R. cantleyi, R. kerrii, R. pricei, and R. keithii (n = 45 in total). Gene Sampling Prior to using mitochondrial (mt) DNA to estimate relationships within Rafflesiaceae, we attempted to ensure that none of the genic regions we isolated were historically horizontally transferred after the origin of the family [3, 4]. To do this, we first performed a preliminary phylogenetic analysis with representatives of all currently recognized monophyletic rosid orders, as well as 2 members of Vitaceae, including the host plant of Rafflesia pricei (Tetrastigma diepenhorstii) so they could be directly compared. For all three mt genes (matR, atp6, and nad1B-C) Rafflesia, Rhizanthes, and Sapria were closely related to each other, and for matR and atp6, the three genera were estimated as members of Malpighiales, as expected [5, 6] (data not shown) suggesting
Fuscopannaria confusa is a rare lichen restricted to very humid localities in boreal forests. Two... more Fuscopannaria confusa is a rare lichen restricted to very humid localities in boreal forests. Two Fuscopannaria species, F. ahlneri and F. mediterranea, and Parmeliella parvula are morphologically problematic to distinguish from F. confusa. Our aim with the present study was to evaluate the taxonomic status of F. confusa and thereby clarify its conservation status in Norway. By phylogenetic analysis of multi-locus DNA sequences, we show that F. confusa is genetically well distinguished from F. ahlneri,F. mediterranea, and P. parvula. Fuscopannaria confusa should therefore be treated as a separate species. A species distribution modelling analysis indicates that F. confusa has a slightly continental but potentially wide geographic distribution in Norway. However, suitable localities are continuously being destroyed by clear-cut logging and hydroelectric power development. Because of the decline in suitable habitats, F. confusa should be regarded as highly threatened in Norway and lis...
ABSTRACT We have addressed phylogenetic relationships and tested hypotheses about five presumed s... more ABSTRACT We have addressed phylogenetic relationships and tested hypotheses about five presumed subgroups among 15 species of Hypocenomyce s.l. (including Pycnora) by use of nuclear (ITS, LSU) and mitochondrial (SSU) ribosomal DNA-regions. Bayesian, likelihood and parsimony phylogenetic analyses, of a dataset with broad Lecanoromycete taxon sampling, mostly support the five presumed subgroups, but two of these were found to be polyphyletic (the H. friesii-group and Pycnora). The seven supported Hypocenomyce s.l. clades belong in different genera, families, orders and even subclasses, and represent a remarkable example of morphological and ecological convergence. Based on our molecular phylogenetic results, we split Hypocenomyce into four genera placed in two subclasses: (1) Carbonicola gen. nov. (Carbonicolaceae fam. nov., Lecanorales, Lecanoromycetidae; including C. anthracophila comb. nov., C. foveata comb. nov., and C. myrmecina comb. nov.); (2) Fulgidea gen. nov. (Umbilicariaceae, Umbilicariales, Umbilicariomycetidae subcl. nov.; including F. oligospora comb. nov. and F. sierrae comb. nov.); (3) Hypocenomyce (Ophioparmaceae, Umbilicariales; including H. australis, H. scalaris, and H. tinderryensis; and (4) Xylopsora gen. nov. (Umbilicariaceae; including X. caradocensis comb. nov. and X. friesii comb. nov.). We split Pycnora into two genera: (1) Pycnora (Pycnoraceae fam. nov., Candelariales, “Candelariomycetidae”; including P. praestabilis, P. sorophora, and P. xanthococca); and (2) Toensbergia gen. nov. (Sporastatiaceae fam. nov., unknown order, ecanoromycetidae; including T. leucococca comb. nov.). We place Hypocenomyce isidiosa in Xylographa (Trapeliaceae, Baeomycetales, Ostropomycetidae; X. isidiosa comb. nov.). We place the Family Ophioparmaceae in the Umbilicariales. Our type studies have shown that the epithet “myrmecina” should replace “castaneocinerea”, and lectotypes are chosen for Lecidea friesii Ach., L. scalaris var. myrmecina Ach., Psora cladonioides var. albocervina Räsänen, and P. cladonioides var. castaneocinerea Räsänen. Elixia cretica is reported as new to North America (from Mexico) and Australia.
Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to... more Brown rot decay removes cellulose and hemicellulose from wood--residual lignin contributing up to 30% of forest soil carbon--and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the "dry…
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