scholarly journals Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision

2018 ◽  
Vol 63 (2) ◽  
pp. 45-64 ◽  
Author(s):  
Jolanta Miadlikowska ◽  
Nicolas Magain ◽  
Carlos J. Pardo-De la Hoz ◽  
Dongling Niu ◽  
Trevor Goward ◽  
...  
Keyword(s):  
High Specificity ◽  
Molecular Data ◽  
Fungal Species ◽  
Bootstrap Support ◽  
Phenotypic Traits ◽  
Phylogenetic Structure ◽  
Putative Species ◽  
Molecular Phylogenetic ◽  
High Bootstrap ◽  
Phylogenetic Revision

AbstractClosely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea.

scholarly journals Fenestelloid clades of the Cucurbitariaceae

2020 ◽  
Vol 44 (1) ◽  
pp. 1-40
Author(s):  
W.M. Jaklitsch ◽  
H. Voglmayr
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Fungal Species ◽  
Lsu Rdna ◽  
Phylogenetic Structure ◽  
Protein Coding ◽  
Molecular Phylogenetic ◽  
Type Studies ◽  
Asexual Morphs ◽  
One New Species

Fresh collections and their ascospore and conidial isolates backed up by type studies and molecular phylogenetic analyses of a multigene matrix of partial nuSSU-, complete ITS, partial LSU rDNA, rpb2, tef1 and tub2 sequences were used to evaluate the boundaries and species composition of Fenestella and related genera of the Cucurbitariaceae. Eight species, of which five are new, are recognised in Fenestella s.str., 13 in Parafenestella with eight new species and two in the new genus Synfenestella with one new species. Cucurbitaria crataegi is combined in Fenestella, C. sorbi in Synfenestella, Fenestella faberi and Thyridium salicis in Parafenestella. Cucurbitaria subcaespitosa is distinct from C. sorbi and combined in Neocucurbitaria. Fenestella minor is a synonym of Valsa tetratrupha, which is combined in Parafenestella. Cucurbitaria marchica is synonymous with Parafenestella salicis, Fenestella bavarica with S. sorbi, F. macrospora with F. media, and P. mackenziei is synonymous with P. faberi, and the latter is lectotypified. Cucurbitaria sorbi, C. subcaespitosa and Fenestella macrospora are lecto- and epitypified, Cucurbitaria crataegi, Fenestella media, F. minor and Valsa tetratrupha are epitypified in order to stabilise the names in their phylogenetic positions. A neotype is proposed for Thyridium salicis. A determinative key to species is given. Asexual morphs of fenestelloid fungi are phoma-like and do not differ from those of other representatives of the Cucurbitariaceae. The phylogenetic structure of the fenestelloid clades is complex and can only be resolved at the species level by protein-coding genes, such as rpb2, tef1 and tub2. All fungal species studied here occur, as far as has been possible to determine, on members of Diaporthales, most frequently on asexual and sexual morphs of Cytospora.

scholarly journals Teloschistaceae (lichenized Ascomycota) from the Galapagos Islands: a phylogenetic revision based on morphological, anatomical, chemical, and molecular data

2020 ◽  
pp. 515-576
Author(s):  
Frank Bungartz ◽  
Ulrik Søchting ◽  
Ulf Arup
Keyword(s):  
New Species ◽  
Taxonomic Revision ◽  
Molecular Data ◽  
New Combinations ◽  
Secondary Chemistry ◽  
Phylogenetic Affiliation ◽  
Molecular Phylogenetic ◽  
Phylogenetic Revision ◽  
A New Species ◽  
Hplc Analyses

The lichen family Teloschistaceae from the Galapagos is revised. Most of the species belong to the Caloplacoideae, two to Teloschistoideae and a few to Xanthorioideae, three subfamilies not validly published, which is remedied here. Four different datasets were analyzed using Bayesian inference. For the bulk of the species, a combined dataset of nrITS, nrLSU and mrSSU was analyzed. Additionally, three analyses were performed using nrITS to further investigate phylogenetic relationships within and between species in each subfamily, and in the genera Xanthomendoza and Squamulea. Four new genera are described: Lacrima, Oceanoplaca, Phaeoplaca, Sucioplaca. Twenty-four species are reported, of which ten are new to science: Caloplaca nigra, Lacrima galapagoensis, Oceanoplaca chemoisidiosa, O. sideritoides, Phaeoplaca tortuca, Squamulea chelonia, S. humboldtiana, S. osseophila, S. oceanica, and Xanthomendoza leoncita. Several new combinations are proposed and three species of Xanthomendoza are reduced to synonymy. Several new combinations and species placed into synonymy do not occur in the Galapagos, but are treated as a consequence of our taxonomic revision. Morphology, anatomy, secondary chemistry, distribution and molecular phylogenetic affiliation are presented for each species and a key is provided. Eight different chemical patterns are quantitatively described based on HPLC analyses. The new genus Lacrima includes L. galapagoensis, a species without vegetative propagules, and two densely isidiate species, L. epiphora and L. aphanotripta that are morphologically similar to ‘Caloplaca’ wrightii. The only species of Galapagos Teloschistaceae that contains xanthones is placed into Huneckia. Oceanoplaca includes two species with the new anthraquinone isidiosin, O. isidiosa and O. chemoisidiosa, while a third species, O. sideritoides, does not contain this secondary metabolite. Phaeoplaca camptidia has previously been reported from Galapagos, but our phylogenetic analysis suggests that it is a new species, here named P. tortuca. An isolated position is occupied by ‘Caloplaca’ diplacia, which we place in it its own monotypic genus Sucioplaca. Some Galapagos Teloschistaceae can be considered a ‘residue’ of unresolved Caloplaca s.l., i.e. the corticolous C. floridana is possibly related to the saxicolous C. nigra, while C. cupulifera can currently not be placed. Squamulea remains particularly problematic and includes S. phyllidizans, that is nested among otherwise unresolved Squamulea species. Based on molecular data, S. phyllidizans is close to ‘Huriella’. ‘Huriella’ flakusii, described from Peru, is confirmed to occur in the Galapagos and the genus is reduced to synonymy with Squamulea. The Squamulea squamosa/subsoluta group remains largely unresolved, but the new species S. chelonia, S. humboldtiana, S. oceanica, and S. osseophila are phylogenetically distinct. Foliose Teloschistaceae are represented only by one species, described as Xanthomendoza leoncita, while the only fruticose species, Teloschistes chrysophthalmus and T. flavicans, are cosmopolitan.

Trechispora yunnanensis sp. nov. (Hydnodontaceae, Basidiomycota) from China

Phytotaxa ◽  
2019 ◽  
Vol 424 (4) ◽  
pp. 253-261 ◽  
Author(s):  
TAI-MIN XU ◽  
YU-HUI CHEN ◽  
CHANG-LIN ZHAO
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Strong Support ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Fungal Species ◽  
Monophyletic Lineage ◽  
Molecular Phylogenetic ◽  
Inference Methods

A new wood-inhabiting fungal species, Trechispora yunnanensis sp. nov., is proposed based on morphological characteristics and molecular phylogenetic analyses. The species is characterized by resupinate basidiomata, rigid and fragile up on drying, cream to pale greyish hymenial surface; a monomitic hyphal system with generative hyphae bearing clamp connections, IKI-, CB-; ellipsoid, hyaline, thick-walled, ornamented, IKI-, CB- basidiospores measuring as 7–8.5 × 5–5.5 µm. The internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood (ML), maximum parsimony (MP) and bayesian inference methods (BPP). The phylogenetic analyses based on molecular data of ITS+nLSU sequences showed that T. yunnanensis formed a monophyletic lineage with a strong support (100% ML, 100% MP, 1.00 BPP) and was closely related to T. byssinella and T. laevis. Both morphological characteristics and results of molecular phylogenetic analyses confirmed the placement of the new species in Trechispora.

Revision of Family Megacalanidae (Copepoda: Calanoida)

Zootaxa ◽  
2017 ◽  
Vol 4229 (1) ◽  
pp. 1 ◽  
Author(s):  
JANET M. BRADFORD-GRIEVE ◽  
LEOCADIO BLANCO-BERCIAL ◽  
GEOFFREY A. BOXSHALL
Keyword(s):  
Cladistic Analysis ◽  
Detailed Examination ◽  
Molecular Data ◽  
Bootstrap Support ◽  
Species Status ◽  
Large Size ◽  
The Family ◽  
High Bootstrap ◽  
Taxonomic Confusion ◽  
Nomen Novum

The Megacalanidae were revised based on new and archived material. Taxonomic confusion that has existed in the family is discussed and a method is suggested for stabilising names. A detailed examination of the morphology of this family, using the light microscope, has added further useful characters that distinguish genera and species. The added, hitherto undescribed species include character states incompatible with aspects of previous generic definitions (e.g. presence or absence of setae on the maxillule coxal endite). Nevertheless, the cladistic and molecular analyses confirmed that there are at least four monophyletic clades mostly with high bootstrap support. These clades represent already defined genera, one of which [Elenacalanus nom. nov. (nomen novum)] replaces the preoccupied name Heterocalanus Wolfenden, 1906. Four previously described species have been re-assigned to Elenacalanus in new combinations: E. princeps (Brady, 1883), E. eltaninae (Björnberg, 1968), E. sverdrupi (Johnson, 1958) and E. inflatus (Björnberg, 1968). Eleven new species are described: three Megacalanus, one Bradycalanus, six Bathycalanus, and one Elenacalanus nom. nov. Bradycalanus pseudotypicus enormis Björnberg, 1968 has been raised to species status based on genetic data although it can be only be distinguished morphologically from Br. typicus by its large size. All four genera are differentially diagnosed and keys are provided to the genera and species. We confirm that all male right antennules are geniculate in the Megacalanidae. Thirteen males are known. Of these males, eight are newly described (M. frosti n. sp., M. ericae n. sp., M. ohmani n. sp., Bathycalanus bradyi (Wolfenden, 1905a), Ba. dentatus n. sp., Ba. milleri n. sp., Ba. unicornis Björnberg, 1968, and Elenacalanus tageae n. sp.). We cannot be absolutely certain that the correct males have been assigned to the appropriate female so our decisions await testing with new data. The cladistic analysis provides the first morphology-based phylogeny. This scheme served as a working hypothesis which was tested and corroborated using the newly gathered molecular data. Vertical and horizontal distributions are summarised. 

scholarly journals ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8392 ◽  
Author(s):  
Janice Valencia-D ◽  
José Murillo-A ◽  
Clara Inés Orozco ◽  
Carlos Parra-O ◽  
Kurt M. Neubig
Keyword(s):  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Bootstrap Support ◽  
Nucleotide Substitutions ◽  
Plastid Genomes ◽  
The Family ◽  
High Bootstrap ◽  
Single Genus

Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.

A molecular phylogenetic analysis of Diuris (Orchidaceae) based on AFLP and ITS reveals three major clades and a basal species

2009 ◽  
Vol 22 (1) ◽  
pp. 1 ◽  
Author(s):  
James O. Indsto ◽  
Peter H. Weston ◽  
Mark A. Clements
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Bootstrap Support ◽  
Its2 Region ◽  
Molecular Phylogenetic ◽  
Strong Bootstrap Support ◽  
Evidence Analysis

Diuris is a terrestrial orchid genus of at least 61 and possibly more than 100 species, restricted to Australia except for one species endemic in Timor. Distinctive species groups have respective eastern and western centres of distribution. Although species affinities have been vaguely understood for many years, no formal infrageneric treatment has been undertaken as Diuris possesses few reliable morphological characters for a classification system. We have undertaken cladistic parsimony and Bayesian phylogenetic analyses of Diuris by using the ITS1–5.8S–ITS2 region of nuclear rDNA and morphological characters, with a subset of samples also studied by amplified fragment length polymorphism (AFLP) as an independent test of phylogenetic relationships. Four major clades with strong bootstrap support were resolved and are named here according to a recently published classification; D. sulphurea forms a lineage (subg. Paradiuris) of its own that is well supported as the sister to the rest of Diuris. Two other major eastern clades contained species related to D. maculata (subg. Xanthodiuris) and D. punctata (subg. Diuris), respectively. Although these latter two subgenera are genetically well resolved, there is minimal genetic variation at species level, consistent with recent, rapid speciation. A fourth clade (subg. Hesperodiuris) has a centre of distribution in Western Australia, and has more genetic and morphological variation than the eastern subgenera. Total evidence analysis provides support for the western clade being sister group to the two eastern subgenera Diuris and Xanthodiuris; however, this relationship was not resolved by molecular data. Hybridisation is known to be common among species within subgenera Diuris and Xanthodiuris. Instances of incongruence between different datasets were found suggestive of hybridisation events between species of different sections of Diuris.

scholarly journals Taxonomic evaluation of selected Ganoderma species and database sequence validation

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3596 ◽  
Author(s):  
Suldbold Jargalmaa ◽  
John A. Eimes ◽  
Myung Soo Park ◽  
Jae Young Park ◽  
Seung-Yoon Oh ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Economic Value ◽  
Elongation Factor ◽  
Distribution Patterns ◽  
Fungal Species ◽  
Morphological Features ◽  
Bootstrap Support ◽  
Translation Elongation ◽  
Identification Of Species ◽  
High Bootstrap

Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily on DNA sequencing using BLAST searches, which are only reliable if the GenBank submissions are accurately labeled. In this study, we examined 113 specimens collected from 1969 to 2016 from various regions in Korea using morphological features and multigene analysis (internal transcribed spacer, translation elongation factor 1-α, and the second largest subunit of RNA polymerase II). These specimens were identified as four Ganoderma species: G. sichuanense, G. cf. adspersum, G. cf. applanatum, and G. cf. gibbosum. With the exception of G. sichuanense, these species were difficult to distinguish based solely on morphological features. However, phylogenetic analysis at three different loci yielded concordant phylogenetic information, and supported the four species distinctions with high bootstrap support. A survey of over 600 Ganoderma sequences available on GenBank revealed that 65% of sequences were either misidentified or ambiguously labeled. Here, we suggest corrected annotations for GenBank sequences based on our phylogenetic validation and provide updated global distribution patterns for these Ganoderma species.

scholarly journals Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 656
Author(s):  
Evangelia Stavridou ◽  
Georgios Lagiotis ◽  
Parthena Kalaitzidou ◽  
Ioannis Grigoriadis ◽  
Irini Bosmali ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Geographical Origin ◽  
Expressed Sequence Tag ◽  
Phenotypic Diversity ◽  
Molecular Data ◽  
Phenotypic Traits ◽  
Dissimilarity Matrix ◽  
Heterotic Groups ◽  
Hrm Analysis ◽  
Sesame Genotypes

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

Integrative taxonomic and geographic variation analyses in Cyrtodactylus aequalis (Squamata: Gekkonidae) from southern Myanmar (Burma): one species, two different stories

2020 ◽  
Vol 66 (3-4) ◽  
pp. 151-179
Author(s):  
L. Lee Grismer ◽  
L. Wood Perry ◽  
Marta S. Grismer ◽  
Evan S.H. Quah ◽  
Myint Kyaw Thura ◽  
...  
Keyword(s):  
Geographic Variation ◽  
Evolutionary History ◽  
Phylogenetic Inference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Biodiversity Crisis ◽  
Allopatric Populations ◽  
Compelling Argument ◽  
Historical Accuracy ◽  
Molecular Phylogenetic

The historical accuracy of building taxonomies is improved when they are based on phylogenetic inference (i.e., the resultant classifications are less apt to misrepresent evolutionary history). In fact, taxonomies inferred from statistically significant diagnostic morphological characters in the absence of phylogenetic considerations, can contain non-monophyletic lineages. This is especially true at the species level where small amounts of gene flow may not preclude the evolution of localized adaptions in different geographic areas while underpinning the paraphyletic nature of each population with respect to the other. We illustrate this point by examining genetic and morphological variation among three putatively allopatric populations of the granite-dwelling Bent-toed Gecko Cyrtodactylus aequalis from hilly regions in southeastern Myanmar. In the absence of molecular phylogenetic inference, a compelling argument for three morphologically diagnosable species could be marshaled. However, when basing the morphological analyses of geographic variation on a molecular phylogeny, there is a more compelling argument that only one species should be recognized. We are cognizant of the fact however, that when dealing with rare species or specimens for which no molecular data are possible, judicious morphological analyses are the only option—and the desired option given the current worldwide biodiversity crisis.

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