Phylogenetic relationships in the tribe Alysseae (Brassicaceae) based on nuclear ribosomal ITS DNA sequences

Botany ◽  
2008 ◽  
Vol 86 (4) ◽  
pp. 315-336 ◽  
Author(s):  
Suzanne I. Warwick ◽  
Connie A. Sauder ◽  
Ihsan A. Al-Shehbaz
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Morphological Characters ◽  
Data Support ◽  
Its Dna Sequences

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 85 species (131 accessions) were used to determine the tribal limits, monophyly status, and phylogenetic intra-tribal relationships of genera within the tribe Alysseae (Brassicaceae). Both maximum parsimony and maximum likelihood analyses support the recognition of the tribe Alysseae s. str. (12 genera: Alyssoides , Alyssum , Aurinia , Berteroa , Bornmuellera , Clastopus , Clypeola , Degenia , Fibigia , Galitzkya , Hormathophylla , and Physoptychis ). Six well-supported clades were recognized within the Alysseae clade, including two Alyssum clades (one of which includes Clypeola ), an Alyssoides and allies clade (includes Alyssoides , Bornmuellera , Clastopus , Degenia , Fibigia , Hormathophylla , and Physoptychis ), a Berteroa and allies clade (includes Aurinia , Berteroa , and Galitzkya ), a Bornmuellera clade, and a Hormathophylla clade. Morphological and cytological support for these clades is reviewed. The ITS data support the exclusion of the following taxa from the Alysseae, with appropriate tribal assignment given in parentheses: Alyssum klimesii Al-Shehbaz (Camelineae), Asperuginoides (unresolved), Athysanus (Arabideae), Botschantzevia (Arabideae), Didymophysa (unresolved), Farsetia (Malcolmieae), Lobularia (Malcolmieae), and Ptilotrichum (Arabideae). Farsetia and Lobularia are inferred to be monophyletic, and based on molecular and morphological characters they are assigned to Malcolmieae, a recently described tribe.

Revisiting the phylogeny and taxonomy of Osmanthus (Oleaceae) including description of the new genus Chengiodendron

Phytotaxa ◽  
2020 ◽  
Vol 436 (3) ◽  
pp. 283-292 ◽  
Author(s):  
YONG-FU LI ◽  
MIN ZHANG ◽  
XIAN-RONG WANG ◽  
STEVEN PAUL SYLVESTER ◽  
QI-BAI XIANG ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
New Genus ◽  
Morphological Character ◽  
Strong Support ◽  
Its Region ◽  
Phylogenetic Placement ◽  
Morphological Patterns

Osmanthus (Oleaceae) is considered one of the most confusing genera with regards to circumscription and phylogenetic placement of taxa within the subtribe Oleinae of Oleaceae, with controversies mainly focused on the attribution of section Leiolea. In the present study, we analyzed 71 samples that represent the broad taxonomic, biogeographic, and morphological patterns in the subtribe Oleinae. Based on concatenation of four plastid genes (trnL-F, trnT-L, trnS-G, and matK) and comparison with the ITS region, Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenies were inferred. Morphological character traits and geographical distributions of taxa were also studied. These results provide strong support for the segregation of the Leiolea clade (Osmanthus marginatus, O. matsumuranus and O. minor) of sect. Leiolea from Osmanthus. Therefore, the Leiolea clade is instated as the new genus Chengiodendron, with a taxonomic treatment provided. This study provides a clearer understanding of the phylogenetic relationships of genera in the subtribe Oleinae.

scholarly journals A Phylogenetic Investigation of the New Zealand  Pteridaceae Ferns

2021 ◽  
Author(s):  
◽  
Whitney L M Bouma
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Native Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Taxonomic Confusion ◽  
Species Specific

<p>The fern family Pteridaceae is among the largest fern families in New Zealand. It comprises 17 native species among five genera. Traditionally the classification of Pteridaceae was based on morphological characters. The advent of molecular technology, now makes is possible to test these morphology-based classifications. The Pteridaceae has previously been subjected to phylogenetic analyses; however representatives from New Zealand and the South Pacific have never been well represented in these studies. This thesis research aimed to investigate the phylogenetic relationships of the New Zealand Pteridaceae, as well as, the phylogenetic relationships of the New Zealand species to their overseas relatives. The DNA sequences of several Chloroplast loci (e.g. trnL-trnF locus, rps4 and rps4-trnS IGS, atpB, and rbcL) were determined and the phylogenetic relationships of the New Zealand Pteridaceae and several species-specific question within the genus Pellaea and Adiantum were investigated. Results presented in this thesis confirm previously published phylogenetics of the Pteridaceae, which show the resolution of five major clades, i.e.,cryptogrammoids, ceratopteridoids, pteridoids, cheilanthoids, and the adiantoids. The addition of the New Zealand species revealed a possible South West Pacific groups formed by the respective genera, where New Zealand species were generally more related to one another than to overseas relatives. Within the New Zealand Pellaea, the analysis of the trnL-trnF locus sequence data showed that the morphologically-intermediate plants P. aff. falcata, responsible for taxonomic confusion, were more closely related to P. rotundifolia than to P. falcata. Furthermore, the species collected on the Kermadec Islands, previously thought to be P. falcata, are genetically distinct from the Australian P. falcata and they could constitute a new species. Adiantum hispidulum, which is polymorphic for two different hair types being used to distinguish them as different species, was also reinvestigated morphologically and molecularly. Morphological inspection of hairs revealed three hair types as opposed to the previous thought two, and furthermore, they correspond to three different trnL-trnF sequences haplotypes.</p>

Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

2009 ◽  
Vol 21 (6) ◽  
pp. 565-570 ◽  
Author(s):  
Kristen L. Kuhn ◽  
Thomas J. Near
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Single Copy ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

Molecular phylogeny of the genus Hylodesmum (Fabaceae)

Phytotaxa ◽  
2019 ◽  
Vol 403 (3) ◽  
pp. 221
Author(s):  
HUAI-CHENG LI ◽  
XUE-LI ZHAO ◽  
XIN-FEN GAO ◽  
BO XU
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Nuclear Marker ◽  
Bayesian Analyses ◽  
Chloroplast Dna Regions ◽  
Taxonomic System

The phylogenetic relationships of 12 Hylodesmum species and closely related genera were reconstructed using maximum parsimony, maximum likelihood, and Bayesian analyses based on two chloroplast DNA regions (rps16-trnQ and trnL-F) and one nuclear marker (internal transcribed spacer, ITS). All analyses yielded reliable relationships among the major lineages within Hylodesmum, suggesting that Hylodesmum is monophyletic. Neither the traditionally defined Desmodium sect. Podocarpium nor D. sect. Repanda within the genus was supported as being monophyletic based on the ITS analyses and the combined ITS and chloroplast dataset analyses. The phylogenetic topologies indicated that the three species included in D. sect. Repanda were separated into different clades, which suggested that D. sect. Repanda is paraphyletic. Generally, the clades retrieved by phylogenetic analyses within D. sect. Podocarpium were consistent with traditionally defined groups except for the American group. The molecular analysis provides information regarding the revision of the traditional taxonomic system of Hylodesmum and for the evaluation of the systematic positions of each species within the genus Hylodesmum.

scholarly journals Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data

MycoKeys ◽  
2019 ◽  
Vol 47 ◽  
pp. 75-95 ◽  
Author(s):  
Ying Zhao ◽  
Xin-zhan Liu ◽  
Feng-yan Bai
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Morphological Characters ◽  
Dna Sequence Data ◽  
D2 Domain ◽  
High Species Diversity ◽  
Molecular Phylogenetic

In the present study, a total of 33 Tremella specimens in China were collected and examined using molecular phylogenetic analysis based on a combined sequence dataset of the nuc rDNA internal transcribed spacer (ITS) region and nuc 28S rDNA D1/D2 domain in conjunction with the morphological characters. Four new species, namely Tremellabasidiomaticola, T.cheejenii, T.erythrina, and T.salmonea, are newly described based on their distinct phylogenetic relationships and the comparison of morphological characters with known Tremella species. Our results indicate a high species diversity of Tremella waiting to be discovered.

scholarly journals A phylogeny of Pouteria (Sapotaceae) from Malesia and Australasia

2007 ◽  
Vol 20 (2) ◽  
pp. 107 ◽  
Author(s):  
Teguh Triono ◽  
Anthony H. D. Brown ◽  
Judy G. West ◽  
Michael D. Crisp
Keyword(s):  
Maximum Parsimony ◽  
Internal Transcribed Spacer ◽  
New Caledonia ◽  
Its Region ◽  
Morphological Characters ◽  
Molecular Data ◽  
High Quality ◽  
Leaf Venation ◽  
Generic Delimitation ◽  
Edible Fruit

The genus Pouteria Aublet is a pantropical group and many of its species produce high-quality timber and edible fruit. In 1991, on the basis of morphological characters, Pennington combined the genus Planchonella Pierre with Pouteria, expanding the latter genus to nine sections and 325 species. However, many Planchonella species were not included in his account and doubt remains about the generic limits of Pouteria sensu Pennington. This paper re-assesses the generic delimitation of Pouteria and its affinities with Planchonella from molecular data generated from the nuclear-encoded internal transcribed spacer (ITS) region. The analysis includes 22 Planchonella species and three Pouteria species sensu van Royen collected from Malesia and Australia, and seven additional Planchonella species from New Caledonia with molecular data available from GenBank. Other genera from Sapotaceae included in the analysis were Chrysophyllum, Niemeyera, Pichonia, Pycnandra and Xantolis (tribe Chrysophylleae) and Mimusops, Palaquium and Manilkara (outgroups from other tribes). The resulting ITS cladograms from both Bayesian and maximum parsimony analyses indicated that Malesian and Australasian Pouteria species are not monophyletic and comprise three separate lineages, therefore providing evidence against the broad circumscription of this genus by Pennington. Tertiary leaf venation type (reticulate, parallel or ramified), when mapped onto the phylogeny, correlated with these groupings, indicating that this character is taxonomically informative.

A preliminary phylogenetic analysis of the genus Fulvius Stål (Hemiptera:Miridae: Cylapinae) based on molecular data

2008 ◽  
Vol 39 (4) ◽  
pp. 407-417 ◽  
Author(s):  
Izabela Sadowska-Woda ◽  
Tobias Malm ◽  
Frédéric Chérot
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Large Subunit ◽  
Morphological Characters ◽  
Molecular Data ◽  
Dna Sequence Data ◽  
Species Groups ◽  
Coi Sequences ◽  
Preliminary Phylogenetic Analysis

AbstractThe systematics and phylogeny of the genus Fulvius Stål remains unclear. We present herein the first analysis of the phylogenetic relationships within the genus Fulvius based on DNA sequences. The phylogenetic interrelationships in the genus Fulvius are investigated using partial DNA sequence data from two mitochondrial genes, the 16S ribosomal large subunit and the cytochrome oxidase I (COI). DNA sequences for Fulvius species representing three different subgroups distinguished previously on the base of morphological characters alone are compared to sequences from the closely related genera Rhinocylapidius and Cylapus. The data are analyzed using parsimony and Bayesian inference. The results confirm that on the basis of molecular data we can distinguish the same congruent groups of Fulvius species as using morphological characters, however with inclusion of the specimens of the genus Rhinocylapidius in the bifenestratus-group. Additional studies are needed to clarify the phylogenetic relationships within the tribe Fulviini, as well as within the genus Fulvius and its relation to Rhinocylapidius. However, the results of this study suggest that 16S and COI sequences will be very useful as molecular markers for such studies among these species-groups.

Phylogeny of the Erysiphales (powdery mildews) inferred from internal transcribed spacer ribosomal DNA sequences

1999 ◽  
Vol 77 (1) ◽  
pp. 150-168 ◽  
Author(s):  
Gregory S Saenz ◽  
John W Taylor
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Powdery Mildews ◽  
Outgroup Species ◽  
Morphological And Molecular Data ◽  
Clade 1

Phylogenetic relationships were inferred for 45 powdery mildews plus two outgroup species from internal transcribed spacer sequence data. Phylogenetic analyses revealed that the powdery mildews formed six evolutionary lineages, which corresponded well to recently revised mitosporic taxa. Clade 1 consisted of Erysiphe, Microsphaera, and Uncinula, all of which have an Oidium subgenus Pseudoidium mitosporic state. Clade 2 consisted of Erysiphe galeopsidis and Erysiphe cumminsiana, which have an Oidium subgenus Striatoidium mitosporic state. Clade 3 consisted of Erysiphe species with an Oidium subgenus Reticuloidium mitosporic state. Clade 4 consisted of Leveillula and Phyllactinia, which have Oidiopsis and Ovulariopsis mitosporic states, respectively. Clade 5 consisted of Sphaerotheca, Podosphaera, and Cystotheca, which have Oidium subgenera Fibroidium and Setoidium mitosporic states. Clade 6 consisted of Blumeria graminis, which has an Oidium subgenus Oidium mitosporic state. Seventeen morphological characters were analysed and found not to conflict with the molecular data, so the morphological and molecular data were combined. The combined data increased the overall support for the six clades.Key words: Ascomycete, Blumeria, Erysiphe, fungi, molecular evolution, plant pathogen.

The genus Marasmius (Basidiomycota, Agaricales, Marasmiaceae) from Republic of São Tomé and Príncipe, West Africa

Phytotaxa ◽  
2019 ◽  
Vol 414 (2) ◽  
pp. 55-104 ◽  
Author(s):  
CHRIS L. GRACE ◽  
DENNIS E. DESJARDIN ◽  
BRIAN A. PERRY ◽  
JACKIE E. SHAY
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Morphological Characters ◽  
Evolutionary Relationships ◽  
Dna Sequence Data ◽  
Sao Tome And Principe ◽  
Dichotomous Key ◽  
Phylogenetic Hypotheses ◽  
New Distribution

This treatise serves as a preliminary monograph and phylogenetic treatment of Marasmius from the African island nation of São Tomé and Príncipe (ST&P), based on data generated from 30 specimens collected in 2008. Twenty-one species are described, seven of which represent species new to science (Marasmius albisubiculosus, M. diversus, M. elaeocephaliformis, M. laranja, M. leptocephalus, M. paratrichotus, M. segregatus), and all represent new distribution records for ST&P. Species are delimited based on comprehensive morphological characters and DNA sequence data. Prior to the collection of these specimens, only one Marasmius species had been documented from these islands. Phylogenetic hypotheses generated from analyses of DNA sequences of the Internal Transcribed Spacer regions (ITS1+5.8S+ITS2) are proposed to explore the evolutionary relationships amongst ST&P Marasmius and global Marasmius diversity. A dichotomous key to aid in identification, illustrations of pertinent micromorphological features, colour photographs of basidiomata, comprehensive descriptions and commentaries are provided.

scholarly journals Phylogenetic relationships of Discyphus scopulariae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences: evidence supporting recognition of a new subtribe, Discyphinae

Phytotaxa ◽  
2014 ◽  
Vol 173 (2) ◽  
pp. 127 ◽  
Author(s):  
GERARDO A. SALAZAR ◽  
Cássio Van den Berg ◽  
ALEX POPOVKIN
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Floral Morphology ◽  
Systematic Position ◽  
Morphological Differences ◽  
Early Radiation ◽  
Molecular Trees

The monospecific genus Discyphus, previously considered a member of Spiranthinae (Orchidoideae: Cranichideae), displays both vegetative and floral morphological peculiarities that are out of place in that subtribe. These include a single, sessile, cordate leaf that clasps the base of the inflorescence and lies flat on the substrate, petals that are long-decurrent on the column, labellum margins free from sides of the column and a column provided with two separate, cup-shaped stigmatic areas. Because of its morphological uniqueness, the phylogenetic relationships of Discyphus have been considered obscure. In this study, we analyse nucleotide sequences of plastid and nuclear DNA under maximum parsimony and maximum likelihood criteria with the aim of clarifying its systematic position and discussing its peculiar morphology in an explicit phylogenetic context. Our analyses failed to support inclusion of Discyphus in Spiranthinae, signifying instead that this genus represents an additional isolated lineage of “core spiranthids.” The notable morphological disparity among such major lineages, as compared with the short internal branches subtending them in the molecular trees, would support the hypothesis that Discyphus represents a relict from an early radiation that also gave rise to Cranichidinae and Spiranthinae, putatively driven by adaptation to different pollinators given the morphological differences in floral morphology among these taxa.

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