Phylogenetic analysis of Andinia (Pleurothallidinae; Orchidaceae) and a systematic re-circumscription of the genus

Most of the species studied in this paper have previously been placed in either Pleurothallis or Lepanthes. However, at one time or another, members of the group have also been placed in the genera Andinia, Brachycladium, Lueranthos, Masdevalliantha, Neooreophilus, Oreophilus, Penducella, Salpistele and Xenosia. Phylogenetic analyses of nuclear ITS and plastid matK sequences indicate that these species form a strongly supported clade that is only distantly related to Lepanthes and is distinct from Pleurothallis and Salpistele. Since this clade includes the type species of Andinia, A. dielsii, and it has taxonomic precedence over all other generic names belonging to this group, Andinia is re-circumscribed and expanded to include 72 species segregated into five subgenera: Aenigma, Andinia, Brachycladium, Masdevalliantha and Minuscula. The required taxonomic transfers are made herein. We hypothesize that convergent evolution towards a similar pollinator syndrome involving deceit pollination via pseudocopulation by Diptera resulted in a similar floral morphology between species of subgenus Brachycladium and species of Lepanthes; hence the prior placement of the species of subgenus Brachycladium in Lepanthes. Species of the re-circumscribed Andinia are confined exclusively to the Andes, ranging from about 1,200 to 3,800 m, from Colombia south to Bolivia, making the generic name very apt. Elevational distributions of the individual clades are discussed in relation to the possible evolutionary diversification of the most species-rich clade, subgenus Brachycladium.

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A phylogenetic analysis and new delimitation of Crepidiastrum (Asteraceae, tribe Cichorieae)

Phytotaxa ◽

10.11646/phytotaxa.159.4.1 ◽

2014 ◽

Vol 159 (4) ◽

pp. 241 ◽

Cited By ~ 7

Author(s):

Yu-lan Peng ◽

Yu Zhang ◽

Xin-fen Gao ◽

Lin-jing Tong ◽

Liang Li ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Maximum Likelihood ◽

Chloroplast Dna ◽

Maximum Parsimony ◽

Phylogenetic Analyses ◽

Systematic Position ◽

Likelihood Inference ◽

Nuclear Its ◽

Chloroplast Dna Regions

The systematic position of Paraixeris humifusa (Asteraceae) is hard to define, because the circumscription of Paraixeris, Youngia and Crepidiastrum, three closely related genera in subtribe Crepidinae (Cichorieae), is not clear. This paper reports on the relationships between 30 species in subtribe Crepidinae, based on an analysis of nucleotides from one nuclear (ITS) and three chloroplast DNA regions ( trnL-F, rps16 and atpB-rbcL). The phylogenetic analyses used maximum parsimony with maximum likelihood inference. The monophyly of Crepidiastrum in the most recent generic classification of Shih & Kilian (2011) is explored. The results show that 12 species in Crepidiastrum constitute a monophyletic group, and that Paraixeris humifusa should be treated as Youngia humifusa.

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Morphological reassessment and molecular assessment of Sargassum (Fucales: Phaeophyceae) species from the Gulf of California, Mexico

Phytotaxa ◽

10.11646/phytotaxa.183.4.1 ◽

2014 ◽

Vol 183 (4) ◽

pp. 201 ◽

Cited By ~ 3

Author(s):

GABRIELA ANDRADE-SORCIA ◽

RAFAEL RIOSMENA-RODRIGUEZ ◽

RAQUEL MUÑIZ-SALAZAR ◽

JUAN MANUEL LÓPEZ-VIVAS ◽

GA HUN BOO ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Brown Algae ◽

Gulf Of California ◽

Phylogenetic Analyses ◽

The Pacific ◽

Pacific Side ◽

Molecular Studies ◽

Molecular Assessment ◽

The Individual

Systematic molecular studies have not been performed on ecologically important brown algae (Sargassum) in the Gulf of California, Mexico, where 42 specific and infraspecific names have been recorded within this genus. We conducted phylogenetic analyses of nuclear ribosomal ITS and mitochondrial cox1 and cox3 sequences, along with detailed morphological observations of Sargassum collected in the Gulf of California. We confirmed the presence of six species, five previously described—S. herporhizum, S. horridum, S. johnstonii, S. lapazeanum, and S. sinicola, as well as the newly described Sargassum ulixei sp. nov. which is characterized by terete primary axes arising from the stipe, lanceolate to elliptical sessile ecostate blades with smooth margins, cryptostomata, ellipsoidal vesicles with a short mucron, and cylindrical to ellipsoidal receptacles. The individual analyses and subsequent phylogenetic analysis recognized two groups previously described by Dawson, one as Sargassum and other as Horridum. Our studies suggest that the Gulf of California is a region with endemic Sargassum species, and is clearly distinguished from the Pacific side of Baja California, where recently introduced species are common. Based on phylogenetic relationships, we propose two geographical origins for the Sargassum from the Gulf of California: a first group originating from the proto-Gulf, related to species from the northern hemisphere (including five species); and a second group, containing S. sinicola, introduced when the southern end opened at a later stage.

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Origin and Isoform Specific Functions of Exchange Proteins Directly Activated by cAMP: A Phylogenetic Analysis

Cells ◽

10.3390/cells10102750 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2750

Author(s):

Zhuofu Ni ◽

Xiaodong Cheng

Keyword(s):

Phylogenetic Analysis ◽

Common Ancestor ◽

Phylogenetic Analyses ◽

Sequence Diversity ◽

Sequence Motifs ◽

Nucleotide Exchange ◽

Animal Kingdom ◽

Specific Sequence ◽

Guanine Nucleotide Exchange ◽

The Individual

Exchange proteins directly activated by cAMP (EPAC1 and EPAC2) are one of the several families of cellular effectors of the prototypical second messenger cAMP. To understand the origin and molecular evolution of EPAC proteins, we performed a comprehensive phylogenetic analysis of EPAC1 and EPAC2. Our study demonstrates that unlike its cousin PKA, EPAC proteins are only present in multicellular Metazoa. Within the EPAC family, EPAC1 is only associated with chordates, while EPAC2 spans the entire animal kingdom. Despite a much more contemporary origin, EPAC1 proteins show much more sequence diversity among species, suggesting that EPAC1 has undergone more selection and evolved faster than EPAC2. Phylogenetic analyses of the individual cAMP binding domain (CBD) and guanine nucleotide exchange (GEF) domain of EPACs, two most conserved regions between the two isoforms, further reveal that EPAC1 and EPAC2 are closely clustered together within both the larger cyclic nucleotide receptor and RAPGEF families. These results support the notion that EPAC1 and EPAC2 share a common ancestor resulting from a fusion between the CBD of PKA and the GEF from RAPGEF1. On the other hand, the two terminal extremities and the RAS-association (RA) domains show the most sequence diversity between the two isoforms. Sequence diversities within these regions contribute significantly to the isoform-specific functions of EPACs. Importantly, unique isoform-specific sequence motifs within the RA domain have been identified.

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Polyphyly of Rulingia and Commersonia (Lasiopetaleae, Malvaceae s.l.)

Australian Systematic Botany ◽

10.1071/sb09030 ◽

2011 ◽

Vol 24 (5) ◽

pp. 215 ◽

Cited By ~ 3

Author(s):

Barbara A. Whitlock ◽

Amanda M. Hale ◽

Jane L. Indorf ◽

Carolyn F. Wilkins

Keyword(s):

Phylogenetic Analysis ◽

Type Species ◽

Phylogenetic Analyses ◽

Chloroplast Markers ◽

Clade 1

The primarily Australian genera Rulingia R.Br. and Commersonia J.R. & G.Forst., as currently circumscribed, are distinguished from each other by the number of antisepalous staminodes. Although most taxonomic treatments recognise Rulingia and Commersonia as separate genera, recent phylogenetic analyses and morphological observations have suggested that neither is monophyletic. In the present study, we test the monophyly of both genera with a phylogenetic analysis of 80 individuals of Rulingia and Commersonia, representing 46 species, using three chloroplast markers. Our analyses recovered the following two well supported clades: Clade 1 includes three species referable to Commersonia and 17 to Rulingia and Clade 2 includes 20 species referable to Commersonia and six to Rulingia. Type species of both Commersonia and Rulingia are in Clade 1, although Commersonia has priority. These results are used to identify lineages that will be formally recognised in accompanying taxonomic treatments. The extensive polyphyly of both Commersonia and Rulingia suggests that the staminode character previously used to separate these two genera is highly homoplastic. We discuss alternative androecial characters that may prove to be synapomorphies for Clades 1 and 2.

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Molecular and morphological phylogenetic analysis and taxonomic revision of the genus Orleanesia (Laeliinae, Epidendroideae, Orchidaceae)

Phytotaxa ◽

10.11646/phytotaxa.392.1.1 ◽

2019 ◽

Vol 392 (1) ◽

pp. 1

Author(s):

GABRIEL F. GONÇALVES ◽

ANNA VICTORIA S. R. MAUAD ◽

GIULIANA TAQUES ◽

ERIC C. SMIDT ◽

FÁBIO DE BARROS

Keyword(s):

Phylogenetic Analysis ◽

Dna Sequences ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Taxonomic Revision ◽

Sister Group ◽

Morphological Data ◽

Data Sets ◽

New Synonyms ◽

Nuclear Its

In order to evaluate the monophyly of the genus Orleanesia (Orchidaceae) and to assess its position within Laeliinae, a phylogenetic analysis was performed using molecular (nuclear ITS and plastid matK DNA sequences) and morphological data. A taxonomic revision of Orleanesia was also performed, with a description of the genus and its species using fresh living plants and 115 exsiccates from 31 herbaria. All phylogenetic analyses were highly congruent, and thus the sequence data from all three data sets were combined. The resulting phylogeny corroborated the monophyly of Orleanesia, with two strongly supported clades, and confirmed Caularthron as its sister group. Character analysis was not very informative due to a high degree of homoplasy. Two lectotypifications and three new synonyms were proposed for the genus, thereby reducing the number of accepted species to six. Although none of the species of Orleanesia are considered endangered, it is clear that some populations are threatened with deforestation and habitat reduction.

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Seifertia shangrilaensis sp. nov. (Melanommataceae), a new species from Southwest China

Phytotaxa ◽

10.11646/phytotaxa.273.1.3 ◽

2016 ◽

Vol 273 (1) ◽

pp. 34 ◽

Cited By ~ 4

Author(s):

JUNFU LI ◽

RUNGTIWA PHOOKAMSAK ◽

AUSANA MAPOOK ◽

SARANYAPHAT BOONMEE ◽

JARAYAMA D. BHAT ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Type Species ◽

Yunnan Province ◽

Southwest China ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Data ◽

New Taxon ◽

A New Species

A new Seifertia species was isolated from hanging rachides of Rhododendron decorum in Yunnan Province, Southwest China. The new taxon was compared with the type species, S. azalea and differs in having wider conidiophores, with hyaline to subhyaline and smaller conidia, while S. azalea has olive-brown to brown, rarely branched conidiophores, and pale brown or olive-brown, very rarely septate conidia. Phylogenetic analyses of combined LSU, SSU and TEF1-α sequence data show that S. shangrilaensis forms a robust clade with S. azalea nested among the species of Melanommataceae in the order Pleosporales. A new species, S. shangrilaensis is introduced in this study, and Seifertia should be placed in Melanommataceae (Pleosporales, Dothideomycetes) based on phylogenetic analysis. Description and illustration of Seifertia shangrilaensis are provided with notes and its introduction is supported by molecular data.

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Re-evaluation of Mycoleptodiscus species and morphologically similar fungi

Persoonia - Molecular Phylogeny and Evolution of Fungi ◽

10.3767/persoonia.2019.42.08 ◽

2019 ◽

Vol 42 (1) ◽

pp. 205-227 ◽

Cited By ~ 12

Author(s):

M. Hernández-Restrepo ◽

J.D.P. Bezerra ◽

Y.P. Tan ◽

N. Wiederhold ◽

P.W. Crous ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Type Species ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Leaf Spots ◽

The Usa ◽

Extensive Collection ◽

One New Species ◽

Type Strains

Mycoleptodiscus includes plant pathogens, animal opportunists, saprobic and endophytic fungi. The present study presents the first molecular phylogeny and revision of the genus based on four loci, including ITS, LSU, rpb2, and tef1. An extensive collection of Mycoleptodiscus cultures, including ex-type strains from the CBS, IMI, MUCL, BRIP, clinical isolates from the USA, and fresh isolates from Brazil and Spain, was studied morphologically and phylogenetically to resolve their taxonomy. The study showed that Mycoleptodiscus sensu lato is polyphyletic. Phylogenetic analysis places Mycoleptodiscus in Muyocopronales (Dothideomycetes), together with Arxiella, Leptodiscella, Muyocopron, Neocochlearomyces, and Paramycoleptodiscus. Mycoleptodiscus terrestris, the type species, and M. sphaericus are reduced to synonyms, and one new species is introduced, M. suttonii. Mycoleptodiscus atromaculans, M. coloratus, M. freycinetiae, M. geniculatus, M. indicus, M. lateralis (including M. unilateralis and M. variabilis as its synonyms) and M. taiwanensis belong to Muyocopron (Muyocopronales, Dothideomycetes), and M. affinis, and M. lunatus to Omnidemptus (Magnaporthales, Sordariomycetes). Based on phylogenetic analyses we propose Muyocopron alcornii sp. nov., a fungus associated with leaf spots on Epidendrum sp. (Orchidaceae) in Australia, Muyocopron zamiae sp. nov. associated with leaf spots on Zamia (Zamiaceae) in the USA, and Omnidemptus graminis sp. nov. isolated from a grass (Poaceae) in Spain. Furthermore, Neomycoleptodiscus venezuelense gen. & sp. nov. is introduced for a genus similar to Mycoleptodiscus in Muyocopronaceae.

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Taxonomy and phylogeny of the genus Steinera (Arctomiales, Arctomiaceae) in the subantarctic islands of Crozet and Kerguelen

Phytotaxa ◽

10.11646/phytotaxa.324.3.1 ◽

2017 ◽

Vol 324 (3) ◽

pp. 201 ◽

Cited By ~ 4

Author(s):

DAMIEN ERTZ ◽

ROAR S. POULSEN ◽

MARYVONNE CHARRIER ◽

ULRIK SØCHTING

Keyword(s):

Convergent Evolution ◽

Type Species ◽

New Genus ◽

Phylogenetic Analyses ◽

Species Group ◽

Phylogenetic Position ◽

The Past ◽

Subantarctic Islands ◽

Species Groups ◽

High Level

The lichenized genus Steinera is revised for the archipelagos of Crozet and of Kerguelen, with a high level of endemism revealed. It is shown to represent a good example of convergent evolution between two different orders. Phylogenetic analyses using nuLSU, RPB1 and mtSSU sequences show that two different species groups can be recognized: Steinera s. str. belongs to the Arctomiaceae (Arctomiales) and is characterized notably by species having pluriseptate ascospores, and a second species group belongs to the Koerberiaceae (Peltigerales) and is characterized notably by simple ascospores sometimes having a plasma-bridge. The genus Henssenia is newly described to accommodate this latter group. The type species of Steinera is shown to have been erroneously treated in the past, with Steinera molybdoplaca being the type of Steinera and “S.” glaucella belonging to the genus Henssenia. A sorediate morph is recorded for S. molybdoplaca and the results confirmed using a 4-gene phylogeny, including nuITS sequences. Some species previously described in the genera Arctomia and Massalongia from the Southern Hemisphere are shown to belong to Steinera s. str. Five new species are described: Steinera isidiata Ertz & R.S. Poulsen, S. membranacea Ertz & R.S. Poulsen, S. lebouvieri Ertz, S. pannarioides Ertz & R.S. Poulsen and Henssenia subglaucella Ertz & R.S. Poulsen along with seven new combinations: Steinera intricata (Øvstedal) Ertz, S. latispora (Øvstedal) Ertz, S. olechiana (Alstrup & Søchting) Ertz & Søchting, S. subantarctica (Øvstedal) Ertz, Henssenia glaucella (Tuck.) Ertz, R.S. Poulsen & Søchting, H. radiata (P. James & Henssen) Ertz and H. werthii (Zahlbr.) Ertz, R.S. Poulsen & Søchting. An epitype is chosen for Henssenia glaucella and a neotype for H. werthii. “Steinera” symptychia has an isolated phylogenetic position in the Koerberiaceae and might represent a distinct, new genus. World-wide identification keys to the species of Henssenia and Steinera are provided.

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Table 1: Phylogeographic, morphometric and taxonomic re-evaluation of the river sardine, Mesobola brevianalis (Boulenger, 1908) (Teleostei, Cyprinidae, Chedrini)

10.21504/rur.12096003.v1 ◽

2020 ◽

Author(s):

Megan A Ridden ◽

Roger Bills ◽

Martin H Villet

Keyword(s):

Phylogenetic Analysis ◽

Cytochrome Oxidase ◽

Southern Africa ◽

Type Species ◽

Phylogenetic Analyses ◽

Cytochrome Oxidase I ◽

Cytochrome Oxidase I Gene ◽

I Gene ◽

Locality Information

<div>The river sardine, Mesobola brevianalis (Boulenger, 1908), is the type species of Mesobola Howes, 1984. Standard phylogenetic analyses of partial sequences of the cytochrome oxidase I gene of individuals from populations across southern Africa that are currently identified as M. brevianalis showed that these populations represent four genetically distinct allopatric lineages. Furthermore, Engraulicypris sardella (Günther, 1868), the type species of Engraulicypris Günther, 1894, was convincingly nested amongst these clades. Table 1. Sample catalogue numbers and locality information for specimens from which DNA was extracted for phylogenetic analysis.</div>

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