Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi

The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.

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Species diversity and genetic differentiation of stygofauna (Syncarida:Bathynellacea) across an alluvial aquifer in north-eastern Australia

Australian Journal of Zoology ◽

10.1071/zo12061 ◽

2012 ◽

Vol 60 (3) ◽

pp. 152 ◽

Cited By ~ 9

Author(s):

B. D. Cook ◽

K. M. Abrams ◽

J. Marshall ◽

C. N. Perna ◽

S. Choy ◽

...

Keyword(s):

Species Diversity ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Alluvial Aquifer ◽

Species Level ◽

Coi Gene ◽

Generic Level ◽

Alluvial Aquifers ◽

Eastern Australia ◽

North Eastern

Recent research suggests that alluvial aquifers in southern and eastern Australia may contain a diverse subterranean aquatic fauna (i.e. stygofauna). However, to date only a limited number of alluvial aquifers have been studied and little molecular data are available to assess species-level diversity and spatial patterns of genetic variation within stygofaunal species. In this paper, we present the initial results of a stygofaunal survey of the Burdekin River alluvial aquifer in Queensland, extending the northern range of alluvial aquifers along the east coast of Australia that have been investigated. The survey resulted in the collection of bathynellid stygofauna (Syncarida: Bathynellacea) and genetic analyses were conducted to determine species level diversity using the mitochondrial cytochrome oxidase subunit I (COI) gene. We further investigated the phylogenetic relationships of the species with bathynellids from western and southern Australia to assess the generic status of species. Four highly divergent COI lineages within the Parabathynellidae and one lineage within the Bathynellidae were found. These lineages did not group within any described genera, and phylogenetic analyses indicated that both local radiations and the retention of a lineage that was more apical in the genealogy account for the diversity within the Parabathynellidae in the Burdekin River alluvial aquifer. Most COI lineages were sampled from only a single bore, although one taxon within the Parabathynellidae was found to be more widespread in the aquifer. Haplotypes within this taxon were not shared among bores (ΦST = 0.603, P < 0.001). Overall, the high species diversity for bathynellaceans from an alluvial aquifer reported here, and surveys of bathynellaceans in several other alluvial systems in south-eastern Australia, suggests that groundwater ecosystems of eastern Australia may contain high stygofaunal diversity by Australian and world standards, particularly at the generic level for parabathynellids.

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PHYLOGENETIC ANALYSIS OF THE AMPHIPOD FAMILY BOGIDIELLIDAE S. LAT., AND REVISION OF TAXA ABOVE THE SPECIES LEVEL

Crustaceana ◽

10.1163/156854099503960 ◽

1999 ◽

Vol 72 (8) ◽

pp. 781-816 ◽

Cited By ~ 15

Author(s):

Stefan Koenemann ◽

John Holsinger

Keyword(s):

Cladistic Analysis ◽

Species Level ◽

Taxonomic Structure ◽

New Genera ◽

Generic Level ◽

The Family ◽

Considerable Confusion ◽

The Status ◽

Group A

AbstractThe increasing number of world-wide discoveries of subterranean amphipods, especially during the last two decades, has led to additions of numerous new taxa in the stygobiont family Bogidiellidae s. lat. To date, the family is composed of 23 genera and 11 subgenera, and approximately 110 described species. However, given the uneven quality of generic and subgeneric diagnoses in the literature, there is considerable confusion regarding the status of some of the taxa at these levels. Even the family itself lacks a clear definition. In order to gain a better knowledge of the phylogeny of this group, a cladistic analysis, employing both PAUP 3.0s and MacClade, was performed on the genera and subgenera currently assigned to the Bogidiellidae s. lat. Supported by the results of this analysis, the taxonomic structure of this group is completely revised above the species level. The revision excludes 5 genera from the family, all remaining subgenera are elevated to generic level. Four taxa are split, resulting in 5 new genera. The family Bogidiellidae now consists of 33 genera. Die wachsende Zahl weltweiter Neuentdeckungen von Grundwasser-Amphipoden, insbesondere wahrend der letzten zwei Jahrzehnte, erweiterte die Stygobiontenfamilie Bogidiellidae s. lat., um zahlreiche neue Taxa. Bis heute sind in der Familie etwa 110 beschriebene Arten in 23 Gattungen und 11 Untergattungen zusammengefasst. Aufgrund der unterschiedlichen Qualitat diagnostischer Beschreibungen herrscht allerdings erhebliche Verwirrung hinsichtlich des taxonomischen Status einiger Gruppen. Sogar die Definition der Familie selbst ist relativ undeutlich. Um neue Einsichten in die Phylogenie der Bogidielliden s. lat., zu erhalten, fuhrten wir eine kladistische Analyse der Gattungen und Untergattungen unter Verwendung der Computerprogramme PAUP 3.0s und MacClade durch. Die Resultate dieser Analyse dienten als hilfreiche Erganzung bei der umfassenden taxonomischen Revision der Gattungen und Untergattungen. Funf Gattungen wurden aus der Familie entfernt und alle Untergattungen zu Gattungen erhoben. Das Aufspalten von vier Taxa resultierte in 5 neuen Gattungen. Die Familie Bogidiellidae besteht somit aus 33 Gattungen.

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Multi-Gene Phylogeny and Morphology Reveal Haplohelminthosporium gen. nov. and Helminthosporiella gen. nov. Associated with Palms in Thailand and A Checklist for Helminthosporium Reported Worldwide

Life ◽

10.3390/life11050454 ◽

2021 ◽

Vol 11 (5) ◽

pp. 454

Author(s):

Sirinapa Konta ◽

Kevin D. Hyde ◽

Samantha C. Karunarathna ◽

Ausana Mapook ◽

Chanokned Senwanna ◽

...

Keyword(s):

New Taxa ◽

Plant Pathogens ◽

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Full Description ◽

New Taxon ◽

New Genera ◽

Diverse Range

Palms (Arecaceae) are substrates for a highly diverse range of fungi. Many species are known as saprobes and many are important plant pathogens. Over the course of our studies of micro-fungi from palms in Thailand, two new taxa were discovered. Morphological characteristics and phylogenetic analyses of combined ITS, LSU, SSU, and tef1-α sequence data revealed their taxonomic positions within Massarinaceae. There are currently ten genera identified and accepted in Massarinaceae, with the addition of the two new genera of Haplohelminthosporium and Helminthosporiella, that are introduced in this paper. Each new genus is provided with a full description and notes, and each new taxon is provided with an illustration for the holotype. A list of identified and accepted species of Helminthosporium with morphology, host information, locality, sequence data, and related references of Helminthosporium reported worldwide is provided based on records in Species Fungorum 2021. This work provides a micro-fungi database of Haplohelminthosporium, Helminthosporiella, and Helminthosporium which can be modified and validated as new data come to light.

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Evolution, characterization and phylogenetic utility of ITS2 gene in Orthoptera and some Polyneoptera: Highly variable at the order level and highly conserved at the species level

Zootaxa ◽

10.11646/zootaxa.4780.1.2 ◽

2020 ◽

Vol 4780 (1) ◽

pp. 54-76

Author(s):

ONUR ULUAR ◽

BATTAL ÇIPLAK

Keyword(s):

Secondary Structure ◽

Nucleotide Sequence ◽

Phylogenetic Analyses ◽

Gc Content ◽

Species Level ◽

Phylogenetic Information ◽

Generic Level ◽

Variable Pattern ◽

Potential Marker ◽

Evolutionary Studies

ITS2 is often suggested as a potential marker for evolutionary studies and species barcoding. However, there are many lineages have not been studied. This study focuses on ITS2 in Polyneoptera at the order and species levels. ITS2 sequences representing six polyneopteran orders and 15 species in the genus Anterastes are studied. We arrived at the following conclusions: (i) ITS2 is highly variable and contains little phylogenetic information in Polyneoptera, (ii) the shortest length and the highest GC content of ITS2 is found in Orthoptera among insects, (iii) the secondary structure exhibits general characteristics of eukaryotes especially in helices II and III, and with no order-specific architecture, (iv) ITS2 is highly conserved at the species level, both in linear sequences and secondary structures, (v) helices I, IA, II, IIA and III almost invariable in nucleotide sequence shared by all species in the genus. At the generic level, the most conspicuous result is the variable pattern in ITS2. It is highly conserved in helical sequences, but highly variable in non/peri-helical regions which we considered to be mutation islands. These frequently mutated regions contain a significant amount of molecular homoplasy, thus, the utility of ITS2 in phylogenetic analyses and species barcoding is low, at least in Polyneoptera.

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Phylogeny, Global Biogeography and Pleomorphism of Zanclospora

Microorganisms ◽

10.3390/microorganisms9040706 ◽

2021 ◽

Vol 9 (4) ◽

pp. 706

Author(s):

Martina Réblová ◽

Miroslav Kolařík ◽

Jana Nekvindová ◽

Andrew N. Miller ◽

Margarita Hernández-Restrepo

Keyword(s):

Dead Wood ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Phenotypic Data ◽

Dna Sequence Data ◽

Plant Matter ◽

Dematiaceous Hyphomycete ◽

Nuclear Loci ◽

Its1 And Its2

Zanclospora (Chaetosphaeriaceae) is a neglected, phialidic dematiaceous hyphomycete with striking phenotypic heterogeneity among its species. Little is known about its global biogeography due to its extreme scarcity and lack of records verified by molecular data. Phylogenetic analyses of six nuclear loci, supported by phenotypic data, revealed Zanclospora as highly polyphyletic, with species distributed among three distantly related lineages in Sordariomycetes. Zanclospora is a pleomorphic genus with multiple anamorphic stages, of which phaeostalagmus-like and stanjehughesia-like are newly discovered. The associated teleomorphs were previously classified in Chaetosphaeria. The generic concept is emended, and 17 species are accepted, 12 of which have been verified with DNA sequence data. Zanclospora thrives on decaying plant matter, but it also occurs in soil or as root endophytes. Its global diversity is inferred from metabarcoding data and published records based on field observations. Phylogenies of the environmental ITS1 and ITS2 sequences derived from soil, dead wood and root samples revealed seven and 15 phylotypes. The field records verified by DNA data indicate two main diversity centres in Australasia and Caribbean/Central America. In addition, environmental ITS data have shown that Southeast Asia represents a third hotspot of Zanclospora diversity. Our data confirm that Zanclospora is a rare genus.

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Biodiversity assessment of ascomycetes inhabiting Lobariella lichens in Andean cloud forests led to one new family, three new genera and 13 new species of lichenicolous fungi

Plant and Fungal Systematics ◽

10.2478/pfs-2019-0022 ◽

2019 ◽

Vol 64 (2) ◽

pp. 283-344

Author(s):

Adam Flakus ◽

Javier Etayo ◽

Jolanta Miadlikowska ◽

François Lutzoni ◽

Martin Kukwa ◽

...

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Great Majority ◽

Morphological Data ◽

New Genera ◽

Cloud Forests ◽

Generic Level ◽

Phenotypic Data ◽

Lichenicolous Fungi ◽

New Family

AbstractNeotropical mountain forests are characterized by having hyperdiverse and unusual fungi inhabiting lichens. The great majority of these lichenicolous fungi (i.e., detectable by light microscopy) remain undescribed and their phylogenetic relationships are mostly unknown. This study focuses on lichenicolous fungi inhabiting the genus Lobariella (Peltigerales), one of the most important lichen hosts in the Andean cloud forests. Based on molecular and morphological data, three new genera are introduced: Lawreyella gen. nov. (Cordieritidaceae, for Unguiculariopsis lobariella), Neobaryopsis gen. nov. (Cordycipitaceae), and Pseudodidymocyrtis gen. nov. (Didymosphaeriaceae). Nine additional new species are described (Abrothallus subhalei sp. nov., Atronectria lobariellae sp. nov., Corticifraga microspora sp. nov., Epithamnolia rugosopycnidiata sp. nov., Lichenotubeufia cryptica sp. nov., Neobaryopsis andensis sp. nov., Pseudodidymocyrtis lobariellae sp. nov., Rhagadostomella hypolobariella sp. nov., and Xylaria lichenicola sp. nov.). Phylogenetic placements of 13 lichenicolous species are reported here for Abrothallus, Arthonia, Globonectria, Lawreyella, Monodictys, Neobaryopsis, Pseudodidymocyrtis, Sclerococcum, Trichonectria and Xylaria. The name Sclerococcum ricasoliae comb. nov. is reestablished for the neotropical populations formerly named S. lobariellum (Sclerococcales). A key to sexual and asexual states of 40 species of lobariellicolous ascomycetous fungi is provided. Teleomorph-anamorph connections were established for several species using molecular methods and/or visual observations in nature. Additionally, we found that the anamorphic species Cornutispora ophiurospora inhabiting Lobariella was often accompanied by ascomata of Spirographa. Results of phylogenetic analyses, including newly generated sequences of several Cornutispora and Spirographa species inhabiting various host lichens, support the conclusion that Cornutispora is a synonym of Spirographa. Our Maximum Likelihood inference based on multiple loci show that all studied Spirographa (including Cornutispora) belong to a new lineage within Ostropales. Based on these highly supported phylogenetic placements and the distinct character states of their conidiomata, in comparison with other Lecanoromycetes, a new family is proposed – Spirographaceae fam. nov. This new lineage includes broadly distributed mycoparasites, inhabiting various lichen and fungal hosts, and representing an early diversification event preceding the lichen-forming clade of Fissurinaceae, Gomphillaceae and Graphidaceae. Two lichenicolous species, Asteroglobulus giselae and Pleoscutula arsenii, were found to be nested within the Spirographa clade, and their teleomorph-anamorph connections were confirmed based on genotypic and phenotypic data. This phylogenetic result is corroborated by their highly similar ascomata anatomy. Together these results strongly indicate that both species are congeneric with Spirographa. As a result, four new species (S. aggregata sp. nov., S. galligena sp. nov., S. maroneae sp. nov., and S. parmotrematis sp. nov.) and 15 new combinations are proposed (Spirographa ascaridiella comb. nov., S. arsenii comb. nov., S. ciliata comb. nov., S. giselae comb. nov., S. herteliana comb. nov., S. hypotrachynae comb. nov., S. intermedia comb. nov., S. lichenicola comb. nov., S. limaciformis comb. nov., S. ophiurospora comb. nov., S. pittii comb. nov., S. pyramidalis comb. nov., S. triangularis comb. nov., S. tricupulata comb. nov., and S. vermiformis comb. nov.). Species of the genus Spirographa, as outlined here, are strongly host-specific, mainly at the generic level of their host. Some host genera can harbour more than one Spirographa species.

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Reclassification of the Sack-bearer Moths (Lepidoptera, Mimallonoidea, Mimallonidae)

ZooKeys ◽

10.3897/zookeys.815.27335 ◽

2019 ◽

Vol 815 ◽

pp. 1-114 ◽

Cited By ~ 5

Author(s):

Ryan A. St Laurent ◽

Akito Y. Kawahara

Keyword(s):

Phylogenetic Analyses ◽

Morphological Characters ◽

Species Level ◽

New Genera ◽

Topological Constraint ◽

Study Results ◽

The Family ◽

Taxonomic Changes ◽

Made In

A backbone molecular phylogeny of Mimallonidae, based on 47 species and 515 loci, was recently published. That study resolved some of the major relationships in the family, but taxon sampling was limited and a classification of the family was not formally presented for all species. Here morphological phylogenetic analyses in parsimony and maximum likelihood (ML) frameworks were conducted that included 192 species and 55 morphological characters. A phylogenetic analysis was also conducted on the morphological dataset with a topological constraint based on the 515 locus tree from the previous study. Results show that nearly all species can be confidently placed in a genus using morphological phylogenetics. The presence of a frenulum, a character that was historically used to distinguish major groups of Mimallonidae, varies within and among genera. Based on our phylogenetic results, the classification of Mimallonidae is revised, which now includes 291 species in 41 genera. Descriptions of three new genera are included: Fatellallagen. n., Citrallagen. n., and Lepismallagen. n. The following taxonomic changes were made in the present article: 43 new/revived combinations (in Aceclostria Vuillot, Arcinnus Herbin, Bedosia Schaus, Bedosiallo St Laurent & Kawahara, Cicinnus Blanchard, Citralla, Druentica Strand, Fatellalla, Lacosoma Grote, Lepismalla, Mimallo Hübner, Procinnus Herbin, Psychocampa Grote, Roelmana Schaus, and Thaelia Herbin), two new species-level synonyms (melini Bryk is synonymized with viemanda Schaus, jaruga Jones is synonymized with hamata Walker), one revived synonymy (roscida Dognin is resynonymized with externa Moore), seven new statuses (in Druentica, Macessoga Schaus, and Trogoptera Herrich-Schäffer), six revived statuses (in Aceclostria, Cicinnus, Druentica, Psychocampa, and Zaphanta Dyar), and one new designation of nomen nudum. In order to alleviate nomenclatural problems, twelve lectotypes are designated (for Tolypidaamaryllis (Schaus), Trogopteraalthora Schaus, Adalgisacroesa Schaus, Alheitapulloides (Dognin), LacosomabriasiaSchaus, Lacosomadiederica Schaus, Lacosomaraydela Schaus, Psychocampalacuna (Schaus), Cicinnuscorallina Dognin, Cicinnuslatris Schaus, Cicinnussolvens Schaus, Cicinnustuisana Schaus) as well as a neotype for Mimallodespecta Walker (= Cicinnusdespecta). This paper also provides apomorphies for each genus and a morphological key to genera. Annotations are given to aid researchers in understanding all changes made herein, and images of male and female and their genitalia are present for nearly all type species.

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From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2005.1735 ◽

2005 ◽

Vol 361 (1465) ◽

pp. 211-225 ◽

Cited By ~ 91

Author(s):

Colin E Hughes ◽

Ruth J Eastwood ◽

C Donovan Bailey

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Related Species ◽

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Species Level ◽

Gene Trees ◽

Closely Related Species ◽

Nuclear Loci

Phylogenetic analyses of DNA sequences have prompted spectacular progress in assembling the Tree of Life. However, progress in constructing phylogenies among closely related species, at least for plants, has been less encouraging. We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. The most popular approach to address this problem has been to use low-copy nuclear genes as a source of DNA sequence data. However, this has had limited success because levels of variation among nuclear intron sequences across groups of closely related species are extremely variable and generally lower than conventionally used loci, and because no universally useful low-copy nuclear DNA sequence loci have been developed. This suggests that solutions will, for the most part, be lineage-specific, prompting a move away from ‘universal’ gene thinking for species-level phylogenetics. The benefits and limitations of alternative approaches to locate more variable nuclear loci are discussed and the potential of anonymous non-genic nuclear loci is highlighted. Given the virtually unlimited number of loci that can be generated using these new approaches, it is clear that effective screening will be critical for efficient selection of the most informative loci. Strategies for screening are outlined.

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Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches

Systematic Biology ◽

10.1093/sysbio/syp021 ◽

2009 ◽

Vol 58 (2) ◽

pp. 240-256 ◽

Cited By ~ 132

Author(s):

William J. Baker ◽

Vincent Savolainen ◽

Conny B. Asmussen-Lange ◽

Mark W. Chase ◽

John Dransfield ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Generic Level

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Mealybug Transmission of Grapevine Leafroll Viruses: An Analysis of Virus–Vector Specificity

Phytopathology ◽

10.1094/phyto-100-8-0830 ◽

2010 ◽

Vol 100 (8) ◽

pp. 830-834 ◽

Cited By ~ 77

Author(s):

Chi-Wei Tsai ◽

Adib Rowhani ◽

Deborah A. Golino ◽

Kent M. Daane ◽

Rodrigo P. P. Almeida

Keyword(s):

Plant Pathogens ◽

Phylogenetic Analyses ◽

Virus Vector ◽

Disease Spread ◽

Virus Species ◽

Vector Species ◽

Vector Transmission ◽

Planococcus Ficus ◽

Grapevine Leafroll Disease ◽

Leafroll Disease

To understand ecological factors mediating the spread of insect-borne plant pathogens, vector species for these pathogens need to be identified. Grapevine leafroll disease is caused by a complex of phylogenetically related closteroviruses, some of which are transmitted by insect vectors; however, the specificities of these complex virus–vector interactions are poorly understood thus far. Through biological assays and phylogenetic analyses, we studied the role of vector-pathogen specificity in the transmission of several grapevine leafroll-associated viruses (GLRaVs) by their mealybug vectors. Using plants with multiple virus infections, several virus species were screened for vector transmission by the mealybug species Planococcus ficus and Pseudococcus longispinus. We report that two GLRaVs (-4 and -9), for which no vector transmission evidence was available, are mealybug-borne. The analyses performed indicated no evidence of mealybug–GLRaV specificity; for example, different vector species transmitted GLRaV-3 and one vector species, Planococcus ficus, transmitted five GLRaVs. Based on available data, there is no compelling evidence of vector–virus specificity in the mealybug transmission of GLRaVs. However, more studies aimed at increasing the number of mealybug species tested as vectors of different GLRaVs are necessary. This is especially important given the increasing importance of grapevine leafroll disease spread by mealybugs in vineyards worldwide.

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