scholarly journals Phylogenetic Relationships in the Genus Rosa Revisited Based on rpl16, trnL-F, and atpB-rbcL Sequences

HortScience ◽  
2015 ◽  
Vol 50 (11) ◽  
pp. 1618-1624 ◽  
Author(s):  
Chengyuan Liu ◽  
Guoliang Wang ◽  
Hui Wang ◽  
Tao Xia ◽  
Shouzhou Zhang ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Maternal Inheritance ◽  
Molecular Level ◽  
Phylogenetic Analyses ◽  
Intergenic Spacer ◽  
Morphological Characters ◽  
Seed Parent ◽  
Molecular Analyses ◽  
Rbcl Sequences

Three chloroplast DNA (cpDNA) sequences [the rpl16 intron, the trnL-F, and atpB-rbcL intergenic spacer (IGS)] were employed to study phylogenetic relationships in the genus Rosa. Phylogenetic analyses using these three concatenated sequences were performed using maximum parsimony (MP) and Bayesian inference (BI) methods. Both analyses results suggest that the molecular phylogeny conforms closely to the conventional classification of botanical sections. Morphological similarities between R. sects. Synstylae and Chinenses, and R. sects. Rosa and Carolinae are corroborated on the molecular level in our analyses. Four taxa from R. sect. Pimpinellifoliae are further divided into two small clades, which reflect the morphological characters for these species on a molecular level. Whereas three accessions of R. foetida from R. sect. Pimpinellifoliae form a separate clade. R. ×fortuniana forms a clade with R. laevigata based on its maternal inheritance of cpDNA. R. ×cooperii is hypothesized to be a hybrid with seed parent from R. sects. Synstylae and Chinenses. And R. roxburghii should be classified as a section within the R. subgen. Rosa, rather than being treated as its own subgenus, based on molecular analyses.

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>

Molecular phylogeny and divergence time estimates in pennatulaceans (Cnidaria: Octocorallia: Pennatulacea)

2020 ◽  
Vol 84 (4) ◽  
pp. 317-330
Author(s):  
Francisco J. García-Cárdenas ◽  
Mónica Núñez-Flores ◽  
Pablo J. López-González
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Soft Bottoms

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times.

Application of cnidae composition in phylogenetic analyses of North Atlantic and Mediterranean dendrophylliid corals (Anthozoa : Scleractinia)

2014 ◽  
Vol 28 (2) ◽  
pp. 214 ◽  
Author(s):  
Irene Martínez-Baraldés ◽  
Pablo J. López-González ◽  
César Megina
Keyword(s):  
Discriminant Analysis ◽  
North Atlantic ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Marine Ecosystems ◽  
Morphological Characters ◽  
Scleractinian Corals ◽  
Molecular Analyses ◽  
The Family ◽  
Morphological Research

Scleractinian corals are widely distributed in all oceans and at all bathymetric levels. Corals are among the most important bio-building organisms in marine ecosystems. The systematics of this hexacoral group is currently undergoing much change owing to studies that combine molecular analyses with morphological research on the calcareous skeletons. However, information from polyp anatomy has been widely ignored, and some aspects, such as the diversity and distribution of the cnidocysts, might help to obtain a better understanding of the relationships at different taxonomic levels. In this study, the cnidocysts of four species of the family Dendrophylliidae (Dendrophyllia ramea, D. cornigera, D. laboreli and Astroides calycularis) are analysed to evaluate the application of cnidae in phylogenetic analyses, and to complete our knowledge of cnidae composition (types, distribution and sizes) for these species. A discriminant analysis based on the cnidae of these species supports the usefulness of these structures. The obtained results indicate that additional morphological characters in scleractinian corals that may help to clarify their phylogenetic relationships can still be found.

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>

scholarly journals Redescription and phylogenetic analyses of Thaparocleidus gomtius and T. sudhakari (Monogenea: Dactylogyridae) from Wallago attu (Siluriformes: Siluridae) in India

2017 ◽  
Vol 54 (1) ◽  
pp. 87-96 ◽  
Author(s):  
C. Verma ◽  
A. Chaudhary ◽  
H. S. Singh
Keyword(s):  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Uttar Pradesh ◽  
18S Rrna Gene ◽  
Morphometric Study ◽  
Rrna Gene ◽  
Molecular Analyses ◽  
Wallago Attu ◽  
Geographical Regions

Summary Two species of Thaparocleidus Jain (1952a) were found harboring W. attu from the Ganga River at two localities, Meerut and Farrukhabad, Uttar Pradesh, India, during the period of 2013-2015. Morphology and morphometric study of specimens identified as Thaparocleidus gomtius (Jain, 1952a) Lim, 1996 and T. sudhakari (Gusev, 1976) Lim, 1996. Molecular analyses using the 18S rRNA gene confirmed the validity of T. gomtius and T. sudhakari and demonstrated that both the species clustered with other Thaparocleidus species from different geographical regions. We aim at reassessing the taxonomy and establishing the phylogenetic relationships among these two redescribed species with other representatives of the genus Thaparocleidus.

Phylogenetic relationships and classification of the Chloropinae of the world (Diptera: Chloropidae)

2020 ◽  
Vol 190 (3) ◽  
pp. 889-941
Author(s):  
Paula Raile Riccardi ◽  
Dalton De Souza Amorim
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Traits ◽  
Analytical Approach ◽  
Morphological Characters ◽  
Phylogenetic Study ◽  
New Genera ◽  
Compelling Evidence ◽  
Incertae Sedis ◽  
The World

Abstract The Chloropidae is a species-rich family of flies with about 3000 species in four subfamilies. The Chloropinae is the second most species-rich subfamily with almost 1000 described species in 75 accepted genera. There is agreement about the monophyly of the subfamily; however, the relationships among the genera are still poorly understood and some genera are clearly paraphyletic. Thus, the interpretation of the evolution of morphological traits, such as male terminalia sclerites, remains challenging. This is the first phylogenetic study of the Chloropinae using a formal analytical approach, including representatives of 73 genera of the subfamily and 124 morphological characters. The monophyly of the Chloropinae is corroborated. Chloropella is sister to the remainder of the subfamily. Slightly different analytical procedures show stable clades and rogue taxa. We propose a system for the subfamily with ten tribes, three of which are newly proposed here—Chloropellini trib. nov., Chloropini, Chloropsinini trib. nov., Diplotoxini, Eurinini stat. nov., Lasiosinini, Mepachymerini, Meromyzini, Mindini and Pseudothaumatomyini. Eight genera are kept incertae sedis and two new genera are erected. There is compelling evidence that Chlorops and Ectecephalina are paraphyletic.

Monophyly of Verbascum (Scrophularieae : Scrophulariaceae): evidence from nuclear and plastid phylogenetic analyses

2014 ◽  
Vol 62 (8) ◽  
pp. 638 ◽  
Author(s):  
Farrokh Ghahremaninejad ◽  
Mehrshid Riahi ◽  
Melina Babaei ◽  
Faride Attar ◽  
Lütfi Behçet ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nrdna Its ◽  
Starting Point ◽  
High Species Diversity ◽  
Phylogenetic Estimation

Verbascum is one of the main genera of Scrophulariaceae, but delimitation and phylogenetic relationships of this genus are unclear and have not yet been studied using DNA sequences. Here, using four selected molecular markers (nrDNA ITS and the plastid spacers trnS/G, psbA-trnH and trnY/T), we present a phylogeny of Verbascum and test previous infrageneric taxonomic hypotheses as well as its monophyly with respect to Scrophularia. We additionally discuss morphological variation and the utility of morphological characters as predictors of phylogenetic relationships. Our results show that while molecular data unambiguously support the circumscription of Verbascum inferred from morphology, they prove to be of limited utility in resolving infrageneric relationships, suggesting that Verbascum ‘s high species diversity is due to rapid and recent radiation. Our work provides phylogenetic estimation of the genus Verbascum using molecular data and can serve as a starting point for future investigations of Verbascum and relatives.

Molecular phylogenetic analyses and morphological variation point to taxonomic problems among four genera of parasitoid doryctine wasps (Hymenoptera : Braconidae)

2015 ◽  
Vol 29 (6) ◽  
pp. 591 ◽  
Author(s):  
Marco Gebiola ◽  
Antonio P. Garonna ◽  
Umberto Bernardo ◽  
Sergey A. Belokobylskij
Keyword(s):  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Evidence ◽  
A Posteriori ◽  
Morphological Examination ◽  
Ongoing Effort ◽  
The Status ◽  
Molecular Phylogenetic

Doryctinae (Hymenoptera : Braconidae) is a large and diverse subfamily of parasitic wasps that has received much attention recently, with new species and genera described and phylogenies based on morphological and/or molecular data that have improved higher-level classification and species delimitation. However, the status of several genera is still unresolved, if not controversial. Here we focus on two related groups of such genera, Dendrosoter Wesmael–Caenopachys Foerster and Ecphylus Foerster–Sycosoter Picard & Lichtenstein. We integrated morphological and molecular (COI and 28S–D2 genes) evidence to highlight, by phylogenetic analyses (maximum likelihood and Bayesian) and a posteriori morphological examination, previously overlooked variation, which is here illustrated and discussed. Monophyly of Dendrosoter and Caenopachys and the presence of synapomorphic morphological characters support synonymy of Caenopachys under Dendrosoter. Low genetic differentiation and high variability for putatively diagnostic morphological characters found in both C. hartigii (Ratzeburg) and C. caenopachoides (Ruschka) supports synonymy of D. caenopachoides under D. hartigii, syn. nov. Morphological and molecular evidence together also indicate independent generic status for Sycosoter, stat. rev., which is here resurrected. This work represents a further advancement in the framework of the ongoing effort to improve systematics and classification of the subfamily Doryctinae.

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