scholarly journals Polyphyly of the genus Canoparmelia—uncovering incongruences between phenotype-based classification and molecular phylogeny within lichenized Ascomycota (Parmeliaceae)

Phytotaxa ◽  
2016 ◽  
Vol 289 (1) ◽  
pp. 36 ◽  
Author(s):  
PAUL M. KIRIKA ◽  
PRADEEP K. DIVAKAR ◽  
ANA CRESPO ◽  
STEVEN D. LEAVITT ◽  
GEORGE MUGAMBI ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Morphological Features ◽  
Evolutionary Relationships ◽  
New Combinations ◽  
Sister Relationship ◽  
Rdna Sequences ◽  
Taxonomic Changes ◽  
Phylogenetic Framework ◽  
Clade 1

Many phenotypical features traditionally used to classify genera in Parmeliaceae and in lichens in general have evolved several times independently, potentially limiting their taxonomic utility. Here, we aim to elucidate evolutionary relationships of Canoparmelia s. lat. among other parmotremoid taxa. A multilocus dataset (ITS, nuLSU and mtSSU rDNA sequences) was gathered and analyzed within a phylogenetic framework. Canoparmelia s. lat. was recovered as highly polyphyletic within the parmelioid clade, and three divergent lineages representing Canoparmelia s. lat. were identified in addition to the previously segregated Crespoa group. Of these, two formed a sister relationship with Parmotrema. However, no apparent diagnostic morphological features were found distinguishing the distinct Canoparmelia s. lat. clades reconstructed in the phylogenetic analyses. As a consequence, we propose to restrict the circumscription of Canoparmelia to clade 1 (i.e. the C. texana group) and to include clades 2 and 3 in Parmotrema. We propose to recognize these well-supported monophyletic clades at subgeneric level. Consequently, the new subgeneric name Parmotrema subgen. Africanae is proposed for clade 3 recovered in this study. Since clade 4, which clusters with the genera Nesolechia and Punctelia, is only represented by a single sequenced specimen, we refrain from proposing any taxonomic changes. The new combinations Parmotrema epileucum, and P. zimbabwense are proposed.

The genus Relicinopsis is nested within Relicina (Parmeliaceae, Ascomycota)

2017 ◽  
Vol 49 (3) ◽  
pp. 189-197 ◽  
Author(s):  
Paul M. KIRIKA ◽  
Pradeep K. DIVAKAR ◽  
Steven D. LEAVITT ◽  
Kawinnat BUARUANG ◽  
Ana CRESPO ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Alternative Hypothesis ◽  
Morphological Features ◽  
Evolutionary Relationships ◽  
New Combinations ◽  
Hypothesis Tests ◽  
Phylogenetic Framework ◽  
Phenotypic Features

AbstractMacro-morphological features traditionally used to segregate genera in Parmeliaceae have been shown to be highly plastic, placing limits on their taxonomic value. Here we aim to elucidate the evolutionary relationships of the genera Relicina and Relicinopsis and reassess the phenotypic features traditionally used to separate these genera. To this end, we gathered ribosomal DNA sequences of ITS, nuLSU and mtSSU and analyzed them in a phylogenetic framework. Relicina was recovered as paraphyletic, with Relicinopsis nested within, and three different clades were identified within Relicina. Alternative hypothesis tests significantly rejected the monophyly of Relicina. Our results indicate that the presence or absence of bulbate cilia is of limited taxonomic value in this clade. Based on differences in conidia, however, we propose to accept Relicinopsis as a subgenus within Relicina as Relicina subgen. Relicinopsis (Elix & Verdon) Kirika, Divakar & Lumbsch. It is proposed that five new combinations of species previously classified in Relicinopsis be placed in Relicina.

scholarly journals A molecular perspective on generic concepts in the Hypotrachyna clade (Parmeliaceae, Ascomycota)

Phytotaxa ◽  
2013 ◽  
Vol 132 (1) ◽  
pp. 21 ◽  
Author(s):  
PRADEEP K. DIVAKAR ◽  
ANA CRESPO ◽  
JANO NÚÑEZ-ZAPATA ◽  
ADAM FLAKUS ◽  
HARRIE J.M. SIPMAN ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
New Combinations ◽  
Generic Delimitation ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Alternative Hypotheses ◽  
Nuclear Its

Recently, molecular phylogenetic studies have revolutionized the generic concepts in Parmeliaceae and in lichen forming fungi in general. In the present study, the generic delimitation in the Hypotrachyna clade is revised using a molecular phylogeny of nuclear ITS, LSU and mitochondrial SSU rDNA sequences of 88 hypotrachynoid taxa. Morphological and chemical features are also revised in each group. 118 sequences are newly generated for this study. Our phylogenetic analyses show the polyphyly of Hypotrachyna as currently circumscribed which falls into four well-supported and one unsupported clade. Cetrariastrum, Everniastrum and Parmelinopsis are nested within Hypotrachyna s. lat., Parmelinopsis being also polyphyletic and nested in one of the Hypotrachyna clades. Cetrariastrum is monophyletic but clustered within Everniastrum. Two alternative hypotheses tests significantly rejected the monophyly of these three genera. As a consequence, the genera Cetrariastrum, Everniastrum, and Parmelinopsis are reduced to synonymy with Hypotrachyna. Furthermore, we here propose an alternative classification to recognize the well-supported clades at subgeneric level and leave the remaining species unclassified within the genus. Five new subgenera are proposed: Hypotrachyna subgen. Cetrariastrum, Hypotrachyna subgen. Everniastrum, Hypotrachyna subgen. Longilobae, Hypotrachyna subgen. Parmelinopsis, and Hypotrachyna subgen. Sinuosae. Forty-nine new combinations are proposed.

scholarly journals Overview and revision of the extant genera and subgenera of Trogidae (Coleoptera: Scarabaeoidea)

2016 ◽  
Vol 47 (1) ◽  
pp. 53-82 ◽  
Author(s):  
Werner P. Strümpher ◽  
Martin H. Villet ◽  
Catherine L. Sole ◽  
Clarke H. Scholtz
Keyword(s):  
Molecular Phylogeny ◽  
Endemic Species ◽  
Strong Support ◽  
Morphological Characters ◽  
New Combinations ◽  
Genus Level ◽  
Generic Rank ◽  
The Family ◽  
Taxonomic Changes

Extant genera and subgenera of the Trogidae (Coleoptera: Scarabaeoidea) are reviewed. Contemporary classifications of this family have been based exclusively on morphological characters. The first molecular phylogeny for the family recently provided strong support for the relationships between morphologically defined genera and subgenera. On the basis of morphological, molecular and biogeographical evidence, certain taxonomic changes to the genus-level classification of the family are now proposed. The family is confirmed as consisting of two subfamilies, Omorginae Nikolajev and Troginae MacLeay, the former with two genera,OmorgusErichson andPolynoncusBurmeister, and the latter with two genera,TroxFabricius andPhoberusMacLeaystat. rev.Phoberusis restored to generic rank to include all Afrotropical (including Madagascan endemic) species;Afromorgusis confirmed at subgeneric rank within the genusOmorgus; and the monotypic Madagascan genusMadagatroxsyn. n.is synonymised withPhoberus.The current synonymies ofPseudotroxRobinson (withTrox),ChesasBurmeister,LagopelusBurmeister andMegalotroxPreudhomme de Borre (all withOmorgus) are all accepted to avoid creating speculative synonyms before definitive phylogenetic evidence is available. New combinations resulting from restoringPhoberusto a monophyletic genus are listed in Appendix A.

scholarly journals Insights on The Morphological and Phylogenetic Delimitation of Dacrymyces Nees

2021 ◽  
Author(s):  
Renato Lúcio Mendes Alvarenga ◽  
Tatiana Baptista Gibertoni
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Features ◽  
New Combinations ◽  
Dna Analyses ◽  
Homogeneous Composition ◽  
Morphological And Molecular Data

Abstract Dacrymycetes has four families and 13 genera, few of them with molecular data available and then usually polyphyletic in phylogenetic analyses. Dacrymyces Nees is one of the polyphyletic genera in Dacrymycetes and it was introduced to accommodate one species, D. stillatus Nees. The morphological features of the genus are a homogeneous composition of the intra-structure and an amphigenous or superior hymenium. In this study, we included Neotropical specimens in the phylogeny of the Dacrymycetes and Dacrymyces s.s. is emended to include species with resupinate basidiomata, unilateral hymenium and heterogeneous context. In this new delimitation, the new species Dacrymyces flavobrunneus is described using morphological and molecular data and three new combinations (D. ceraceus comb. nov., D. maxidorii comb. nov. and D. spathularia comb. nov.) are proposed based on DNA analyses.

scholarly journals An SSU rDNA barcoding approach to the diversity of marine interstitial cercozoans, including descriptions of four novel genera and nine novel species

2010 ◽  
Vol 60 (8) ◽  
pp. 1962-1977 ◽  
Author(s):  
Chitchai Chantangsi ◽  
Brian S. Leander
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Environmental Dna ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Morphological Features ◽  
Molecular Signature ◽  
Nucleotide Sequence Analysis ◽  
Heterotrophic Flagellates ◽  
Rdna Sequences

Environmental DNA surveys have revealed a great deal of hidden diversity within the Cercozoa. An investigation into the biodiversity of heterotrophic flagellates in marine benthic habitats of British Columbia, Canada, demonstrated the presence of several undescribed taxa with morphological features that resemble the cercozoan genera Cryothecomonas and Protaspis. Nine novel species of marine interstitial cercozoans are described that are distributed into five genera, four of which are new. Phylogenetic analyses of small subunit rDNA sequences derived from two uncultured isolates of Protaspis obliqua and nine novel cercozoan species (within four novel genera) provided organismal anchors that helped establish the cellular identities of several different environmental sequence clades. These data, however, also showed that the rarity of distinctive morphological features in cryomonads, and other groups of cercozoans, makes the identification and systematics of the group very difficult. Therefore, a DNA barcoding approach was applied as a diagnostic tool for species delimitation that used a 618 bp region at the 5′ end of the SSU rDNA sequence. Nucleotide sequence analysis of this region showed high intergeneric sequence divergences of about 7 % and very low intraspecific sequence divergences of 0–0.5 %; phylogenetic analyses inferred from this barcoding region showed very similar tree topologies to those inferred from the full-length sequence of the gene. Overall, this study indicated that the 618 bp barcoding region of SSU rDNA sequences is a useful molecular signature for understanding the biodiversity and interrelationships of marine benthic cercozoans.

scholarly journals NEW COMBINATIONS IN LOMATIUM (APIACEAE, SUBFAMILY APIOIDEAE)

Phytotaxa ◽  
2017 ◽  
Vol 316 (1) ◽  
pp. 95 ◽  
Author(s):  
MARY ANN E. FEIST ◽  
JAMES F. SMITH ◽  
DONALD H. MANSFIELD ◽  
MARK DARRACH ◽  
RICHARD P. MCNEILL ◽  
...  
Keyword(s):  
North American ◽  
Phylogenetic Analyses ◽  
New Combinations ◽  
Taxonomic Changes ◽  
Endemic Genera ◽  
State Regional

Molecular and morphological phylogenetic analyses indicate that many of the perennial endemic genera of North American Apiaceae are either polyphyletic or nested within paraphyletic groups. In light of these results, taxonomic changes are needed to ensure that ongoing efforts to prepare state, regional, and continental floristic treatments of Apiaceae reflect recent findings. Thus, six new combinations are made to accommodate the movement of five taxa from their current assignment into the genus Lomatium and the elevation of one variety of Lomatium to the level of species; Lomatium lithosolamans, Lomatium tenuissimum, Lomatium fusiformis, Lomatium linearifolium, Lomatium multifidum, and Lomatium planosum.

Taxonomic revision and phylogeny of the ant genus Prenolepis (Hymenoptera: Formicidae)

Zootaxa ◽  
2016 ◽  
Vol 4200 (2) ◽  
pp. 201 ◽  
Author(s):  
JASON L. WILLIAMS ◽  
JOHN S. LAPOLLA
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
New Combination ◽  
New Combinations ◽  
Extant Species ◽  
Morphological Diagnosis ◽  
Taxonomic Changes ◽  
Inference Methods ◽  
Worker Caste

The formicine ant genus Prenolepis is here revised for the first time. Thirteen extant species are recognized of which four are described as new. A key for the worker caste is provided, and the worker of each species is imaged, with males and queens imaged in species where they are known. Worker-based characters were used to construct a species-level phylogeny of Prenolepis. Both maximum parsimony and Bayesian inference methods were used for the phylogenetic analyses. A morphological diagnosis for the genus is provided, with a discussion of useful morphological characters for separating Prenolepis from other genera in the Prenolepis genus-group. Major taxonomic changes are proposed. The new species are: P. darlena, P. fustinoda, P. mediops, and P. shanialena. Prenolepis jerdoni subopaca is elevated to full species. Three species are excluded from Prenolepis and transferred to Nylanderia and Paratrechina as new combinations: N. emmae, N. flaviabdominis, and P. umbra. Two species are excluded from Paratrechina and transferred to Nylanderia and Paraparatrechina as new combinations: N. guanyin and P. kongming. One species, Z. darlingtoni, is excluded from Nylanderia and transferred to Zatania as a new combination. Several synonyms are proposed: Prenolepis sphingthoraxa = Nylanderia flaviabdominis; P. imparis arizonica, P. imparis colimana, P. imparis coloradensis, and P. imparis veracruzensis = P. imparis; P. melanogaster carinifrons and P. nigriflagella = P. melanogaster; P. longiventris and P. magnocula = P. naoroji; and P. septemdenta = Nylanderia opisopthalmia. 

scholarly journals A revision of the minor species group in the millipede genus Nannaria Chamberlin, 1918 (Diplopoda, Polydesmida, Xystodesmidae)

ZooKeys ◽  
2021 ◽  
Vol 1030 ◽  
pp. 1-180
Author(s):  
Jackson C. Means ◽  
Derek A. Hennen ◽  
Paul E. Marek
Keyword(s):  
Molecular Phylogeny ◽  
Species Group ◽  
Distribution Maps ◽  
Aposematic Coloration ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Group A ◽  
Taxonomic Changes ◽  
Phylogenetic Framework ◽  
Genus One

Millipedes in the family Xystodesmidae (Polydesmida) are often referred to as “colorful, flat-backed millipedes” for their bright aposematic coloration and tendency to form Müllerian mimicry rings in the Appalachian region. However, there are many species of Xystodesmidae that do not display colorful warning patterns, and instead have more cryptic appearances. Perhaps for this reason, groups such as the genus Nannaria have remained understudied, despite containing a large number of undescribed species. Before his death in 2012, R. L. Hoffman worked on a revision of the genus Nannaria, and synthesized material and drawings since 1949. Here the work is continued, inferring a molecular phylogeny of the Nannariini (Nannaria + Oenomaea pulchella), and revealing two clades within the genus. One clade is named the minor species group, and the second is the wilsoni species group. This revision, using a molecular phylogenetic framework, is the basis for descriptions of 35 new species in the minor species group. A multi-gene molecular phylogeny is used to make taxonomic changes in the taxon. Eleven putative species of Nannaria are also illustrated and discussed. Additionally, detailed collection, natural history and habitat notes, distribution maps, and a key to species of the Nannaria minor species group are provided. These items are synthesized as a basis for a revision of the genus, which hopefully will aid conservation and evolutionary investigations of this cryptic and understudied group.

Morphology and molecular phylogeny reveal two new species in Russula sect. Ingratae from China

Phytotaxa ◽  
2021 ◽  
Vol 525 (2) ◽  
pp. 109-123
Author(s):  
BIN CHEN ◽  
JIE SONG ◽  
JIN-HUA ZHANG ◽  
JUN-FENG LIANG
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
New Taxa ◽  
Phylogenetic Analyses ◽  
Morphological Features ◽  
Pale Yellow ◽  
Light Yellow ◽  
Two New Species ◽  
Yellowish White

Two new species of Russula are described and illustrated in this paper. Russula clavulus is recognised by a pale yellow pileus centre, white margin with tuberculate striation, white to pale lamellae with small pale yellow spots, white to light yellow spore print, subglobose to broadly ellipsoid spores with short or long ridges and hymenial cystidia on lamellae sides that are mainly subclavate or fusiform. Russula multilamellula is morphologically characterised by the brownish orange to hazel pileus centre and satin white to yellowish-white margin with brownish tinge, lamellulae that are usually irregular in length and often anastomosing with lamellae, subglobose to broadly ellipsoid spores with short or long ridges and clavate hymenial cystidia. The combination of morphological features and multigene phylogenetic analyses of ITS-nrLSU-RPB2-mtSSU data indicated that these two new taxa belong to Russula subg. Heterophyllidia sect. Ingratae.

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