Phylogenetic relationships in subtribe Poinae (Poaceae, Poeae) based on nuclear ITS and plastid trnT–trnL–trnF sequencesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (8) ◽  
pp. 938-967 ◽  
Author(s):  
Lynn J. Gillespie ◽  
Robert J. Soreng ◽  
Roger D. Bull ◽  
Surrey W.L. Jacobs ◽  
Nancy F. Refulio-Rodriguez
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Close Relationships ◽  
Sequence Data ◽  
New Combination ◽  
Special Issue ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Nuclear Its ◽  
Selection Of

The worldwide temperate subtribe Poinae comprises the largest grass genus, Poa (500+ species), and multiple additional small genera. We explore generic boundaries and relationships among genera of Poinae using nuclear ribosomal internal transcribed spacer data (ITS) and plastid trnT–trnL–trnF (TLF) sequence data. ITS and TLF analyses are mostly congruent with regards to circumscription of genera, and with respect to relationships among Poinae genera, but tree structure is generally better supported among genera in the ITS strict consensus tree. ITS and TLF both support two main Poinae lineages: (i) Poa and (ii) a clade comprising all other sampled Poinae. Nine small genera were nested within the large Poa clade, including Aphanelytrum , Dissanthelium , and Tovarochloa , supporting inclusion of these as sections within Poa. In the second clade, three subclades support close relationships among Nicoraepoa , Hookerochloa , and Arctagrostis ; Arctophila and Dupontia ; and Apera , Bellardiochloa , and Ventenata . Genera of the related subtribes Alopecurinae, Cinninae, and Miliinae were mixed among or in part external to Poinae in different ways in ITS and TLF analyses, and only subtribe Puccinelliinae was strongly supported and monophyletic. ITS analyses supported placement of Catabrosella , Hyalopoa , and Paracolpodium in Puccinelliinae (no TLF data available). The position of Poa subgenus Arctopoa is incongruent between the two analyses: TLF data support inclusion within Poa and ITS data place it outside of Poa. Similarly, TLF data resolves the genus Aniselytron outside of Poa, whereas ITS data place it within Poa. Based on these results and a consideration of morphology, we recognize Arctopoa and Aniselytron as genera, probably of ancient hybrid origins. Nothogenus  × Duarctopoa is coined for Arctopoa × Dupontia, with a single nothospecies  × Duarctopoa labradorica . A new combination is provided for Poa subg. Sylvestres .

Species delimitation, phylogenetic relationships, and two new species in the Cuscuta gracillima complex (Convolvulaceae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 670-681 ◽  
Author(s):  
Mihai Costea ◽  
Fiona Aiston ◽  
Saša Stefanović
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Species Delimitation ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Conservation Status ◽  
Special Issue ◽  
Dna Sequence Data ◽  
F Region ◽  
Selection Of

Basic morphology, scanning electron microscopy, and DNA sequence data from the plastid trnL–F region and the nuclear internal transcribed spacer (ITS) regions were used to delimit the species of a recently circumscribed clade of Cuscuta (Convolvulaceae) and to investigate their phylogenetic relationships. This clade comprises the Cuscuta gracillima complex from Mexico, Central and northern South America, a group which is characterized by inflorescences that appear to emerge directly from the host stem. Eight lineages are recognized, with two of them described here as new species: Cuscuta punana Costea & Stefanović, sp. nov. from Ecuador and Cuscuta vandevenderi Costea & Stefanović, sp. nov. from Mexico. Cuscuta colombiana Yunck is redefined to include Cuscuta aristeguietae Yunck., and Cuscuta deltoidea Yunck. is broadened to encompass Cuscuta serruloba Yunck. A taxonomic treatment with an identification key, descriptions, and illustrations is provided; the biogeography and conservation status of the eight species are also discussed.

Phylogenetic relationships of the neuropogonoid core group in the genus Usnea(Ascomycota: Parmeliaceae)

2011 ◽  
Vol 43 (6) ◽  
pp. 553-559 ◽  
Author(s):  
H.Thorsten LUMBSCH ◽  
Nora WIRTZ
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Strong Support ◽  
New Combination ◽  
Bayesian Analyses ◽  
Core Group ◽  
Dna Sequence Data ◽  
The Core ◽  
Statistical Confidence ◽  
Nuclear Its

AbstractSpecies of Usnea with black pigmentation in the cortex and dark apothecial discs are informally referred to as neuropogonoid lichens. Here we studied the phylogenetic relationships of the core group of neuropogonoid lichens using DNA sequence data of three loci: nuclear ITS and IGS rDNA and RPB1. Maximum likelihood and Bayesian analyses revealed monophyly of 11 neuropogonoid species, with U. ciliata and U. subcapillaris forming a separate lineage. The backbone of the phylogeny of the core group was not resolved with statistical confidence, but relationships of groups of two to three species received strong support (U. acromelana +U. aurantiaco-atra; U. messutiae+U. pallidocarpa; U. sphacelata+U. subantarctica+U. trachycarpa; U. lambii+U. perpusilla+U. ushuaiensis). The new combination U. lambii (Imshaug) Wirtz & Lumbsch comb. nov. is made and U. messutiae Wirtz & Lumbsch sp. nov. is described.

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

Phylogenetic relationships among families of the order Anomopoda (Crustacea, Branchiopoda, Cladocera)

Zootaxa ◽  
2004 ◽  
Vol 760 (1) ◽  
pp. 1 ◽  
Author(s):  
LOURDES M.A. ELMOOR-LOUREIRO
Keyword(s):  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Trunk Limbs ◽  
Trunk Limb

The phylogenetic relationships among families of the Order Anomopoda (Crustacea, Branchiopoda, Cladocera) were investigated through a cladistic analysis including 93 characters and 37 terminal taxa (2 as outgroups). The strict consensus tree supported the monophyly of the Anomopoda and its families, and indicated the existence of two main clades: (Moinidae+Daphniidae) and (Dumontidae (Ilyocryptidae+Bosminidae+Radopoda)). The later clade was supported by trunk limb characters, probably related to life associated with the bottom or with macrophytes (lifestyle lost in Bosminidae, but still visible in some of its trunk limbs). Within the Radopoda, the Eurycercoidea was monophyletic, but the monophyly of the Macrothricoidea was not supported.

Cortinarius rapaceoides, a new record for Turkey

Mycotaxon ◽  
2020 ◽  
Vol 135 (3) ◽  
pp. 559-568
Author(s):  
Meryem Senay Şengul Demirak ◽  
Hakan Işik
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
New Record ◽  
Sequence Data ◽  
Large Subunit ◽  
Morphological Description ◽  
Molecular Evidence

A macrofungus collected from Akbelen village in Tokat has been identified based on molecular evidence and morphology as Cortinarius rapaceoides, a new record from Turkey. Sequence data generated from the nuclear ribosomal internal transcribed spacer and ribosomal large subunit regions were deposited in GenBank and used to determine phylogenetic relationships within Cortinarius subg. Phlegmacium. A morphological description, illustrations, and phylogeny of the Turkish C. rapaceoides are provided.

Phylogenetic relationships in the genus Crinum (Amaryllidaceae) with emphasis on tropical African species: evidence from trnL-F and nuclear ITS DNA sequence data

Taxon ◽  
2007 ◽  
Vol 56 (3) ◽  
pp. 801-810 ◽  
Author(s):  
Ezekeil G. Kwembeya ◽  
Charlotte S. Bjorå ◽  
Brita Stedje ◽  
Inger Nordal
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
African Species ◽  
Dna Sequence Data ◽  
Nuclear Its

scholarly journals Phylogenetic relationships within the Pylochelidae (Decapoda: Anomura: Paguroidea): A cladistic analysis based on morphological characters

Zootaxa ◽  
2009 ◽  
Vol 2022 (1) ◽  
pp. 1-14 ◽  
Author(s):  
RAFAEL LEMAITRE ◽  
PATSY A. MCLAUGHLIN ◽  
ULF SORHANNUS
Keyword(s):  
Hermit Crab ◽  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Data Matrix ◽  
Parsimony Analysis ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
The Family

Phylogenetic relationships within the “symmetrical” hermit crab family Pylochelidae were analyzed for 41 of the 45 species and subspecies currently considered valid. In the analyses, 78 morphological characters comprised the data matrix and the outgroup consisted of Thalassina anomala, a member of the Thalassinidae, and Munida quadrispina, a member of the Galatheidae. A poorly resolved strict consensus tree was obtained from a heuristic parsimony analysis of unweighted and unordered characters, which showed the family Pylochelidae and the subfamilies Pylochelinae and Pomatochelinae to be monophyletic taxa – the latter two groups had the highest Bremer support values. Additionally, while the subgenus Pylocheles (Pylocheles) was strongly supported, the subgenera Xylocheles, and Bathycheles were not. More fully resolved trees were obtained when using implied weighting, which recognized the monotypic subfamilies Parapylochelinae, Cancellochelinae and Mixtopagurinae. The subfamily Trizochelinae was found to have four distinct clades and several ambiguously placed taxa.

Culture experiments and DNA sequence data confirm the identity of Lobaria photomorphs

2003 ◽  
Vol 81 (3) ◽  
pp. 232-247 ◽  
Author(s):  
Soili Stenroos ◽  
Elfriede Stocker-Wörgötter ◽  
Isao Yoshimura ◽  
Leena Myllys ◽  
Arne Thell ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Green Alga ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Its Rdna ◽  
Dna Sequence Data

Lichens consist of a fungal component that associates with either a green alga or cynobacterium, resulting in diverse morphologies. Resynthesis experiments of isolated myco- and photobionts, as well as internal transcribed spacer (ITS) rDNA phylogenies, suggest that the notoriously dissimilar photomorphs of Lobaria fendleri (Tuck. ex Mont.) Lindau and Lobaria amplissima (Scop.) Forss. both have a single mycobiont, which can simultaneously lichenize two unrelated photobionts, a eukaryote and a prokaryote. In the phylogenetic analyses, the genera Sticta and Durietzia appear monophyletic; whereas Lobaria and Pseudocyphellaria are both nonmonophyletic. Furthermore, the phylogenetic relationships of Durietzia, Lobarina, and Sticta relative to Lobaria and Pseudocyphellaria are in need of re-evaluation.Key words: internal transcribed spacer (ITS), photosymbiodeme, phylogeny, lichen-forming fungi, Lobaria amplissima, Lobaria fendleri, Pseudocyphellaria, Sticta.

scholarly journals An appraisal of the phylogenetic relationships of Hypoptopomatini cascudinhos with description of two new genera and three new species (Siluriformes: Loricariidae)

2017 ◽  
Vol 15 (4) ◽  
Author(s):  
Maria Laura S. Delapieve ◽  
Pablo Lehmann A ◽  
Roberto E. Reis
Keyword(s):  
New Species ◽  
New Taxa ◽  
Retention Index ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Data Matrix ◽  
New Genera ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Three New Species

ABSTRACT The discovery of three new taxa of Hypoptotopomatini with ambiguous generic assignment prompted a reanalysis of the phylogenetic relationships of the tribe. The analysis focused on a data matrix of 56 terminals and 107 morphological characters comprising the three new taxa, most species of Hypoptopoma and Otocinclus, and all other species of the tribe. The 162 maximally parsimonious trees of 382 steps, consistency index of 0.41, and retention index of 0.83 were then summarized in a strict consensus tree. The results confirm the monophyly of the Hypoptopomatini, recover four genera as monophyletic (Acestridium, Hypoptopoma, Niobichthys, and Otocinclus), revealed Hypoptopoma and Oxyropsis to be non-monophyletic; and revealed two new genera within Hypoptopomatini. Additionally, Otocinclus was found to be sister to a group with all remaining genera of the tribe; Acestridium and Niobichthys were found to be sister to each other and that clade sister to a group formed by ((Leptotocinclus + Hypoptopoma [part]) + (Nannoxyropsis (Oxyropsis + Hypoptopoma [part]))). Based on this framework, changes to the classification and the taxonomy of the Hypoptopomatini are suggested and the new taxa are described.

Phylogenetic Relationships in Helianthus (Asteraceae) Based on Nuclear Ribosomal DNA Internal Transcribed Spacer Region Sequence Data

1998 ◽  
Vol 23 (2) ◽  
pp. 177 ◽  
Author(s):  
Edward E. Schilling ◽  
C. Randal Linder ◽  
Richard D. Noyes ◽  
Loren H. Rieseberg
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Nuclear Ribosomal Dna ◽  
Internal Transcribed Spacer Region ◽  
Region Sequence
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