Molecular systematics of the Acmena alliance (Myrtaceae): phylogenetic analyses and evolutionary implications with reference to Australian taxa

2004 ◽  
Vol 17 (1) ◽  
pp. 63 ◽  
Author(s):  
M. G. Harrington ◽  
P. A. Gadek
Keyword(s):  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Molecular Systematics ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Morphological Features ◽  
Parsimony Analysis ◽  
Species Groups ◽  
Difficult Sequences

The existence within Australia of several Acmena alliance taxa with morphological features inconsistent with current generic boundaries has meant that phylogenetic assessment of relationships has proved difficult. Sequences of nrDNA from the ITS and ETS regions were obtained for 66 Australian taxa, including representatives from both subfamilies and five genera. The ingroup taxa included 54 Australian endemics and 13 species with distributions that also range outside continental Australia. Parsimony analysis and Bayesian inference of posterior possibilities from the combined molecular datasets do not correlate with the species associations implied by the current taxonomic circumscription of genera: Acmena, Acmenosperma, Anetholea, Syzygium and Waterhousea. The molecular phylogeny recognises five supported lineages within the Acmena alliance, and several novel species associations. The recognition of five species groups indicates a need for a reappraisal of all currently recognised morphological groups within the alliance.

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.

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.

Molecular phylogeny and morphology of Cunninghamella guizhouensis sp. nov. (Cunninghamellaceae, Mucorales), from soil in Guizhou, China

Phytotaxa ◽  
2020 ◽  
Vol 455 (1) ◽  
pp. 31-39
Author(s):  
ZHI-YUAN ZHANG ◽  
YI-XUAN ZHAO ◽  
XIN SHEN ◽  
WAN-HAO CHEN ◽  
YAN-FENG HAN ◽  
...  
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Sequence Data ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Keratinolytic Fungi ◽  
A New Species ◽  
Shape And Size

During a survey of keratinolytic fungi in China, three Cunninghamella strains were isolated. Phylogenetic analyses of ITS and ITS+LSU+EF-1α sequence data showed that these strains constitute a new species related to C. blakesleeana, C. bigelovii, C. multiverticillata and C. phaeospora. The new species differs from C. multiverticillata and C. phaeospora in the shape and size of its teminal and lateral vesicles and can be distinguished from C. blakesleeana and C. bigelovii by the absent of zygosporangia, and the shape and size of it sporangioles. The results of phylogenetic and morphological analyses indicate that the three strains are a new species of Cunninghamella. Descriptions and illustrations of this novel species are provided in this paper.

Molecular systematics of Dolichopodidae (Diptera) inferred from COI and 12S rDNA gene sequences based on European exemplars

2007 ◽  
Vol 21 (5) ◽  
pp. 453 ◽  
Author(s):  
Marco Valerio Bernasconi ◽  
Marc Pollet ◽  
Paul Irvine Ward
Keyword(s):  
Molecular Systematics ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Current Position ◽  
European Species ◽  
12S Rdna ◽  
Stable Species ◽  
The Family ◽  
Species Groups

With ~7000 species in ~220 genera, the Dolichopodidae is one of the most speciose families of Diptera. Though the family as such is well defined, knowledge on the internal phylogenetic relationships is generally poor and although authors of successive monographs and catalogues indifferently listed most genera in specific subfamilies, their decisions were rarely based on sound phylogenetic analyses and never on molecular data. In a first attempt to unravel the phylogeny of Dolichopodidae, a combined COI + 12S rDNA dataset (1199 characters) of 119 samples of 101 European species was used in Bayesian (BAY), neighbour joining (NJ) and weighted/unweighted maximum parsimony analyses (MP). At the subfamily level, our study supports the monophyly of Dolichopodinae, Sympycninae, and Hydrophorinae (including Machaerium Haliday, 1832). Ten (Campsicnemus Haliday, 1851, Chrysotus Meigen, 1824, Dolichopus Latreille, 1796, Gymnopternus Loew, 1857, Medetera Fischer von Waldheim, 1819, Poecilobothrus Mik, 1878, Rhaphium Meigen, 1803, Teuchophorus Loew, 1857, Sciapus Zeller, 1842, Syntormon Loew, 1857) of the 14 multispecies genera formed monophyletic assemblages in all analyses and relationships among Argyra Macquart, 1834 species were supported in most analyses. At the subgeneric level, seven of the nine stable species-groups in Dolichopus as established during previous research were supported in most analyses. The validity of the recent transfer of Hercostomus chrysozygos Wiedemann, 1817 to Poecilobothrus was clearly supported in all analyses. Within Argyra and Rhaphium, interspecific relationships reflected previously used subgeneric classifications (Lasiargyra Mik, 1878, Leucostola Loew, 1857 and Argyra s.s. in Argyra; Porphyrops Meigen, 1824, Rhaphium s.s. and Xiphandrium Loew, 1857 in Rhaphium). Further, subclades within Medetera corresponded to species-groups defined by other authors featuring a different morphology and ecology. Anepsiomyia flaviventris (Meigen, 1824) most probably does not belong to Sympycninae but its current position within Peloropeodinae could not be confirmed.

Amphibambusa hongheensis sp. nov., a novel bambusicolous ascomycete from Yunnan, China

Phytotaxa ◽  
2021 ◽  
Vol 505 (2) ◽  
pp. 201-212
Author(s):  
HONG-BO JIANG ◽  
SHI-JIE ZHANG ◽  
RUNGTIWA PHOOKAMSAK ◽  
ITTHAYAKORN PROMPUTTHA ◽  
PATTANA KAKUMYAN ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Yunnan Province ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Novel ◽  
Molecular Approach ◽  
Mucilaginous Sheath ◽  
Phylogenetic Affinity ◽  
First Time

Amphibambusa hongheensis sp. nov. was collected from dead bamboo culms in Honghe County of Yunnan Province, China. The novel species is introduced based on the morpho-molecular approach. Morphologically, A. hongheensis fits well with Amphibambusa and is characterized by immersed, globose to subglobose ascomata, with protruding carbonaceous papilla, unitunicate, cylindrical to elongate fusiform, subsessile to short pedicellate asci with a J+, subapical ring, and fusiform, hyaline to pale brown, 1-septate ascospores, longitudinally striated, and surrounded by a thick mucilaginous sheath. Phylogenetic analyses of a concatenated ITS-LSU sequence dataset based on maximum-likelihood and Bayesian inference criteria revealed the phylogenetic affinity of A. hongheensis within Cainiaceae (Xylariales, Sordariomycetes). Amphibambusa hongheensis formed an independent subclade sister to A. bambusicola with moderate support (81% ML, 0.96 PP) and clustered with the genus Arecophila in Cainiaceae. Amphibambusa hongheensis is the second species accommodated in Amphibambusa and is reported from Yunnan, China, for the first time. Detailed description, illustration and updated phylogeny are provided.

scholarly journals Taxonomy, ontogeny and molecular phylogeny of Anteholosticha marimonilata spec. nov. (Ciliophora, Hypotrichida) from the Yellow Sea, China

2011 ◽  
Vol 61 (8) ◽  
pp. 2000-2014 ◽  
Author(s):  
Yuan Xu ◽  
Jie Huang ◽  
Xiaozhong Hu ◽  
Khaled A. S. Al-Rasheid ◽  
Weibo Song ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Yellow Sea ◽  
Gene Sequence ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Sequence Information ◽  
Rrna Gene Sequence ◽  
Cortical Granules

The morphology, morphogenesis and molecular phylogeny of the marine ciliated protozoan Anteholosticha marimonilata spec. nov., isolated from mollusc-farming waters of the Yellow Sea, Qingdao, PR China, were investigated using microscopic observations of live and protargol-impregnated specimens and by small subunit rRNA gene sequence analysis. The novel species could be distinguished by the following features: an elongated elliptical body, in vivo size 80–160 µm × 30–50 µm; an adoral zone consisting of about 36 membranelles; three frontal, one parabuccal, one buccal, two frontoterminal and usually two pretransverse ventral cirri; 10–13 transverse cirri; a midventral complex composed of 12–17 pairs of cirri only, terminating in posterior 1/5; four or five dorsal kineties; two types of colourless cortical granules; four to nine moniliform macronuclear nodules and one to three micronuclei, and a contractile vacuole positioned at mid-body. Hitherto, the ontogenesis of the genus Anteholosticha has been regarded as rather diverse, which was confirmed by the morphogenetic processes of this novel species. The most noteworthy feature of A. marimonilata was that the proter retained almost the entire parental adoral zone except for a few proximal membranelles that were renewed in situ. The SSU rRNA gene sequence information clearly discriminated this isolate from its congeners. Molecular phylogenetic analyses demonstrated, with high statistical support, that A. marimonilata branched as a sister lineage to the Nothoholosticha–Pseudokeronopsis clade and hence belongs to the core part of the order Urostylida.

scholarly journals Morphology, morphogenesis and molecular phylogeny of a novel soil ciliate, Pseudouroleptus plestiensis n. sp. (Ciliophora, Oxytrichidae), from the uplands of Colfiorito, Italy

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2625-2635 ◽  
Author(s):  
Daizy Bharti ◽  
Santosh Kumar ◽  
Antonietta La Terza
Keyword(s):  
Molecular Phylogeny ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
The Novel ◽  
Gene Sequences ◽  
Ssu Rrna Gene ◽  
Umbria Region ◽  
The Right

The terrestrial oxytrichid ciliate Pseudouroleptus plestiensis n. sp., isolated from soil samples collected from the uplands of Colfiorito (Umbria region, Italy), was investigated using live observation and protargol impregnation. The morphology, morphogenesis and molecular phylogeny inferred from small-subunit (SSU) rRNA gene sequences were studied. The novel species is mainly characterized by the following: a cell size of about 145×35 µm in vivo; two ellipsoidal macronuclear nodules and two to four micronuclei; adoral zone about 26 % of body length with a mean of 30 membranelles; about 40 cirri in the right marginal row and 38 in the left marginal row; left fronto-ventral row consisting of about 27–40 cirri, right fronto-ventral row of about three to seven cirri forming a short row to the right of the rear portion of the left fronto-ventral row; one parabuccal cirrus ( = III/2), one buccal and one post-peristomial cirrus; and four dorsal kineties with caudal cirri at the end of kineties 1 and 2. The morphogenesis of the novel species is similar to that of Pseudouroleptus caudatus. Phylogenetic analyses based on SSU rRNA gene sequences consistently placed the novel species within the family Oxytrichidae Ehrenberg, 1838, clustering with P. caudatus and the genus Strongylidium. The results from the present study contribute to the expanding knowledge of the diversity of ciliates in Italian soil.

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.

Taxonomy and phylogenetic appraisal of Leptosphaeria chatkalica sp. nov. (Leptosphaeriaceae, Pleosporales) from Uzbekistan

Phytotaxa ◽  
2021 ◽  
Vol 520 (2) ◽  
pp. 155-168
Author(s):  
ANIS S. LESTARI ◽  
DHANUSHKA N WANASINGHE ◽  
YUSUFJON GAFFOROV ◽  
DANUSHKA S. TENNAKOON ◽  
K. W. THILINI CHETHANA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Sequence Data ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Tien Shan ◽  
The Novel ◽  
Mucilaginous Sheath ◽  
Tien Shan Mountains ◽  
Comprehensive Characterization

Leptosphaeria chatkalica, found on dead stems of dicotyledon from Chatkal ridge of Western Tien Shan Mountains in Uzbekistan, is presented as a novel species based on morphological details and multi-locus phylogenetic analyses. Phylogenetic relationships of the novel species were established by analyzing the combined sequence data of LSU, ITS, SSU and tef1-α in Maximum parsimony, Maximum likelihood and Bayesian inference analyses. Leptosphaeria chatkalica is characterized by perithecial ascomata, club-like pedicel asci and yellowish-brown, 3-septate, fusiform ascospores with a mucilaginous sheath. A comprehensive characterization and micro-graphs, together with a comparison with other Leptosphaeria species are given.

Reassessing taxonomic relationships in the Berkheya clade (Asteraceae, Arctotideae–Gorteriinae): the utility of achene morphology

Phytotaxa ◽  
2016 ◽  
Vol 246 (1) ◽  
pp. 1
Author(s):  
Ntombifikile Phaliso ◽  
Robert James McKenzie ◽  
Noluthando C Netnou-Nkoana ◽  
Per Ola Karis ◽  
Nigel P Barker
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Species Relationships ◽  
Infrageneric Classification ◽  
Phylogenetic Reconstructions ◽  
Infraspecific Taxa ◽  
Molecular Phylogenetic ◽  
Species Groups ◽  
Species Grouping

The genus Berkheya is paraphyletic with the related genera Cullumia, Cuspidia, Didelta and Heterorhachis embedded within a broader clade termed the ‘Berkheya clade’. As a contribution towards reassessment of species relationships and delimitation of species groupings within the clade, the utility of external achene morphology for supporting natural species groups within the clade was evaluated. Achenes from 67 species and 10 infraspecific taxa were examined, including representatives of each genus currently recognised in the Berkheya clade. Achene pubescence and pappus characteristics (e.g., scale shape and number of scales within a series) were indicated to be particularly variable and thus less reliable for assessment of species relationships. Of the currently recognised genera, only segregation of Cullumia was supported by achene and pappus characteristics. Species groupings implicit in Roessler’s infrageneric classification of eight series within Berkheya were to a large extent supported. However, in particular, series Speciosae was indicated to be a disparate species grouping and the distinction of series Angustae and Cruciatae is not supported by achene and pappus morphology. Achene and pappus characteristics suggest several novel species groupings (e.g. an affinity between Berkheya cuneata, B. ferox and B. spinosa). Although the taxonomic sampling in published molecular phylogenetic analyses is limited, achene and pappus morphology partially supports clades resolved in prevailing phylogenetic reconstructions for the clade. More complete sampling in future molecular phylogenetic analyses is required to test novel species affinities suggested in the present study and to explore the evolution of the achene and pappus in the Berkheya clade.

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