Size doesn´t matter—recircumscription of Microlejeunea (Lejeuneaceae, Porellales) based on molecular and morphological evidence

Phytotaxa ◽  
2013 ◽  
Vol 85 (2) ◽  
pp. 41 ◽  
Author(s):  
SHANSHAN DONG ◽  
ALFONS SCHÄFER-VERWIMP ◽  
TAMÁS PÓCS ◽  
KATHRIN FELDBERG ◽  
ALEKSANDRA CZUMAJ ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Morphological Evidence ◽  
Its2 Region ◽  
Rbcl Gene ◽  
F Region

Phylogenetic analyses of a three marker dataset of Lejeuneaceae (chloroplast genome rbcL gene and trnL-F region, and nuclear ribosomal ITS1-5.8S-ITS2 region) resolve the “Lejeunea complex” in three main lineages assigned here to Harpalejeunea, Lejeunea and Microlejeunea. The taxa Harpalejeunea fischeri, H. filicuspis, H. latitans and Pluvianthus squarrosus are nested in a clade with several representatives of Microlejeunea including the generitype M. africana, and are transferred to the latter genus. Harpalejeunea and Microlejeunea differ from Lejeunea by the presence of ocelli. Harpalejeunea has diverging, blunt underleaf lobes in contrast to the forward directed, blunt to acute underleaf lobes of Microlejeunea. Morphologically similar accessions of Microlejeunea form independent lineages. Drepanolejeunea vandenberghenii is newly reported for Madagascar, Malawi and Réunion.

Transfer of Lejeunea huctumalcensis to Physantholejeunea (Lejeuneaceae, Porellales)

2013 ◽  
Vol 26 (5) ◽  
pp. 386 ◽  
Author(s):  
Aleksandra Czumay ◽  
Shanshan Dong ◽  
Armin Scheben ◽  
Alfons Schäfer-Verwimp ◽  
Kathrin Feldberg ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Morphological Evidence ◽  
Its2 Region ◽  
Rbcl Gene ◽  
Molecular Phylogenetic

Phylogenetic analyses of a three-marker dataset of Lejeuneaceae (chloroplast genome rbcL gene and trnL–trnF region, and nuclear ribosomal ITS1–5.8S-ITS2 region) resolve Lejeunea huctumalcensis (synonym Ceratolejeunea dussiana) in a well supported lineage with Physantholejeunea portoricensis. Representatives of Lejeunea and Ceratolejeunea form independent lineages. Physantholejeunea and L. huctumalcensis share the presence of ocelli, pycnolejeuneoid innovations and keeled perianths, with keels forming horn-like projections. On the basis of the molecular phylogenetic and morphological evidence, we transfer L. huctumalcensis to Physantholejeunea.

New insights on Hygrophorus penarioides and H. penarius (Agaricales, Hygrophoraceae) from Hungary

Phytotaxa ◽  
2019 ◽  
Vol 392 (2) ◽  
pp. 127
Author(s):  
ERIK ZAJTA ◽  
TORDA VARGA ◽  
GÁBOR M KOVÁCS ◽  
BÁLINT DIMA
Keyword(s):  
Sequence Variation ◽  
Geographical Origin ◽  
Phylogenetic Analyses ◽  
Morphological Variability ◽  
Strong Support ◽  
Morphological Evidence ◽  
Its2 Region ◽  
Herbarium Specimens ◽  
Nrdna Its ◽  
Nrdna Its Regions

The ectomycorrhiza forming basidiomycete Hygrophorus penarius sensu lato was recognized as two species, H. penarioides and H. penarius in 2007 based on molecular and morphological evidence. However, this was based on few collections of restricted geographical origin and no studies have performed molecular analysis on additional specimens to date.To this end we sequenced the nrDNA ITS regions of 29 H. penarius s. l. collections from Hungary and Slovakia and analysed with collections from previous studies. Bayesian and Maximum Likelihood phylogenetic analyses confirmed the separation of H. penarioides and H. penarius in two clades with the majority of the specimens belonging to H. penarioides and only three to H. penarius. Despite the strong support of the lineages, there was no coherent difference in basidiome and spore traits. We also provide the first evidence of an intraspecific nrDNA sequence variation in the ITS2 region of H. penarioides together with morphological variability that has not been reported to date.On the basis of our result, we conclude that the Quercus associated H. penarioides is far more common in Hungary than the Fagus associated H. penarius and we suggest that identification of the two species in the absence of DNA sequence analysis should be handled with caution, especially when herbarium specimens are examined.

scholarly journals A 150 year-old mystery solved: Transfer of the rheophytic endemic liverwort Myriocolea irrorata to Colura

Phytotaxa ◽  
2012 ◽  
Vol 66 (1) ◽  
pp. 55 ◽  
Author(s):  
JOCHEN HEINRICHS ◽  
SHANSHAN DONG ◽  
YING YU ◽  
ALFONS SCHÄFER-VERWIMP ◽  
TAMÁS PÓCS ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Rbcl Gene ◽  
Molecular Topology ◽  
F Region ◽  
Large Size ◽  
Molecular Dataset

Myriocolea irrorata is an endemic rheophytic liverwort known from a few localities in the Eastern Andes of Ecuador. Morphologically it belongs to the Cololejeunea-Tuyamaella clade of Lejeuneaceae, however, due to its exclusively Radula-type branching, transversely inserted, hollow leaves, large size, and an extremely high number of clustered gynoecia it has often been regarded as an isolated element of this group. Phylogenetic analyses of a molecular dataset consisting of three markers (nuclear ribosomal ITS region, plastidic trnL-F region and rbcL gene) and 20 accessions resolved Myriocolea in one of the main clades of Colura, sister to the generitype Colura calyptrifolia. Based on the molecular topology and a reinterpretation of morphological traits, Myriocolea irrorata is transferred to Colura, as Colura irrorata. The example Myriocolea/Colura adds to growing evidence that rheophytic liverworts may develop unusual morphologies that hamper their classification using exclusively morphology.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

scholarly journals Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 744
Author(s):  
Yunyan Zhang ◽  
Yongjing Tian ◽  
David Y. P. Tng ◽  
Jingbo Zhou ◽  
Yuntian Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Eastern China ◽  
Chloroplast Microsatellites ◽  
Endangered Tree ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications ◽  
Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

scholarly journals Chloroplast genome variation and phylogenetic relationships of Atractylodes species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiheng Wang ◽  
Sheng Wang ◽  
Yanlei Liu ◽  
Qingjun Yuan ◽  
Jiahui Sun ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Herbal Medicines ◽  
Structural Genomic ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Original Plant ◽  
Morphological Differences ◽  
Rna Genes

Abstract Background Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the universal DNA barcodes cannot clearly distinguish the systemic relationship or identify the species of the genus. In order to solve these question, we sequenced the chloroplast genomes of all species of Atractylodes using high-throughput sequencing. Results The results indicate that the chloroplast genome of Atractylodes has a typical quadripartite structure and ranges from 152,294 bp (A. carlinoides) to 153,261 bp (A. macrocephala) in size. The genome of all species contains 113 genes, including 79 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Four hotspots, rpl22-rps19-rpl2, psbM-trnD, trnR-trnT(GGU), and trnT(UGU)-trnL, and a total of 42–47 simple sequence repeats (SSR) were identified as the most promising potentially variable makers for species delimitation and population genetic studies. Phylogenetic analyses of the whole chloroplast genomes indicate that Atractylodes is a clade within the tribe Cynareae; Atractylodes species form a monophyly that clearly reflects the relationship within the genus. Conclusions Our study included investigations of the sequences and structural genomic variations, phylogenetics and mutation dynamics of Atractylodes chloroplast genomes and will facilitate future studies in population genetics, taxonomy and species identification.

Morphology and phylogeny of Halamphora yongxingensis sp. nov. (Bacillariophyta), a new marine benthic diatom isolated from Yongxing Island, South China Sea

Phytotaxa ◽  
2015 ◽  
Vol 195 (1) ◽  
pp. 53 ◽  
Author(s):  
Hai-ying Jiang ◽  
Chao-qun Hu ◽  
Hai-peng Yang ◽  
Lv-ping Zhang ◽  
Peng-fei Peng ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
South China Sea ◽  
South China ◽  
18S Rdna ◽  
Phylogenetic Analyses ◽  
Light And Electron Microscopy ◽  
Benthic Diatom ◽  
Rbcl Gene ◽  
China Sea ◽  
Morphological Differences

Halamphora yongxingensis sp. nov., a marine benthic diatom isolated from an intertidal reef around the Yongxing Island, South China Sea (16° 58’ 43.3” N, 112° 14’ 41.7” E), is described in this study on the basis of light and electron microscopy. This diatom is also compared with related taxa such as Halamphora subturgida (Hustedt) Levkov and Amphora subtropica Wachnicka & Gaiser. In addition, phylogenetic analyses based on 18S rDNA and rbcL gene were also conducted. The results revealed that H. yongxingensis was clustered into the Halamphora clade, closely related to Halamphora montana (Krasske) Levkov. We discuss morphological differences between H. yongxingensis and H. montana.

Tigridiopalma longmenensis (Melastomataceae), a new species from Guangdong, China

Phytotaxa ◽  
2021 ◽  
Vol 500 (3) ◽  
pp. 241-247
Author(s):  
HUI-FENG WANG ◽  
ZHENG-FENG WANG ◽  
QIAO-MEI QIN ◽  
HONG-LIN CAO ◽  
XIAO-MING GUO
Keyword(s):  
New Species ◽  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Monotypic Genus ◽  
Distribution Map ◽  
Complete Chloroplast Genome ◽  
Chloroplast Genomes ◽  
A New Species

Tigridiopalma longmenensis, a new species from Guangdong, China, is described. This species differs from its ally, T. magnifica, by the polychasium consisting of scorpioid cymes, hypanthium with carinas on angles, and longer stamens with a conspicuously white or pink spur at the connective base of anther. A diagnosis and a distribution map of the two species are also provided. The complete chloroplast genome of T. longmenensis was reported here. Phylogenetic analyses based on complete chloroplast genomes from T. longmenensis and other 15 Melastomataceae species indicated that T. longmenensis is sister to T. magnifica. The discovery of T. longmenensis terminates Tigridiopalma as a monotypic genus.

Molecular systematics of Thouarella (Octocorallia:Primnoidae) with the description of three new species from the Southern Ocean based on combined molecular and morphological evidence

2021 ◽  
Author(s):  
Mónica Núñez-Flores ◽  
Daniel Gomez-Uchida ◽  
Pablo J. López-González
Keyword(s):  
New Species ◽  
Southern Ocean ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Weddell Sea ◽  
Morphological Evidence ◽  
Three New Species ◽  
Taxonomic Framework ◽  
The Antarctic

Thouarella Gray, 1870, is one of the most speciose genera among gorgonians of the family Primnoidae (Cnidaria:Octocorallia:Anthozoa), being remarkably diverse in the Antarctic and sub-Antarctic seafloor. However, their diversity in the Southern Ocean is likely underestimated. Phylogenetic analyses of mitochondrial and nuclear DNA markers were integrated with species delimitation approaches as well as morphological colonial and polyps features and skeletal SEM examinations to describe and illustrate three new species within Thouarella, from the Weddell Sea, Southern Ocean: T. amundseni sp. nov., T. dolichoespinosa sp. nov. and T. pseudoislai sp. nov. Our species delimitation results suggest, for the first time, the potential presence of Antarctic and sub-Antarctic cryptic species of primnoids, based on the likely presence of sibling species within T. undulata and T. crenelata. With the three new species here described, the global diversity of Thouarella has increased to 41 species, 15 of which are endemic to the Antarctic and sub-Antarctic waters. Consequently, our results provide new steps for uncovering the shelf benthonic macrofauna’s hidden diversity in the Southern Ocean. Finally, we recommend using an integrative taxonomic framework in this group of organisms and species delimitation approaches because the distinctions between some Thouarella species based only on a superficial examination of their macro- and micromorphological features is, in many cases, limited.

Elusive Relationships Within Order Fabales: Phylogenetic Analyses Using matK and rbcL Sequence Data

2009 ◽  
Vol 34 (1) ◽  
pp. 102-114 ◽  
Author(s):  
M. A. Bello ◽  
A. Bruneau ◽  
F. Forest ◽  
J. A. Hawkins
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Evidence ◽  
Taxon Sampling ◽  
Rapid Radiation ◽  
Bayesian Approaches ◽  
Molecular Studies ◽  
Alternative Hypotheses ◽  
The One ◽  
Good Support

The order Fabales, including Leguminosae, Polygalaceae, Quillajaceae and Surianaceae, represents a novel hypothesis emerging from angiosperm molecular phylogenies. Despite good support for the order, molecular studies to date have suggested contradictory, poorly supported interfamilial relationships. Our reappraisal of relationships within Fabales addresses past taxon sampling deficiencies, and employs parsimony and Bayesian approaches using sequences from the plastid regions rbcL (166 spp.) and matK (78 spp.). Five alternative hypotheses for interfamilial relationships within Fabales were recovered. The Shimodaira-Hasegawa test found the likelihood of a resolved topology significantly higher than the one calculated for a polytomy, but did not favour any of the alternative hypotheses of relationship within Fabales. In the light of the morphological evidence available and the comparative behavior of rbcL and matK, the topology recovering Polygalaceae as sister to the rest of the order Fabales with Leguminosae more closely related to Quillajaceae + Surianaceae, is considered the most likely hypothesis of interfamilial relationships of the order. Dating of selected crown clades in the Fabales phylogeny using penalized likelihood suggests rapid radiation of the Leguminosae, Polygalaceae, and (Quillajaceae + Surianaceae) crown clades.

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