scholarly journals Jumping through the hoops: the challenges of daffodil (Narcissus) classification

2019 ◽  
Vol 190 (4) ◽  
pp. 389-404 ◽  
Author(s):  
Kálmán Könyves ◽  
John David ◽  
Alastair Culham
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Plastid Dna ◽  
Microsatellite Data ◽  
Population Sampling ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Nuclear Microsatellite ◽  
Congruent Group ◽  
First Time

Abstract Hoop-petticoat daffodils are a morphologically congruent group comprised of two distinct lineages in molecular phylogenetic trees of Narcissus. It is possible that the morphological similarity is a product of both historic and current low-level gene flow between these lineages. For the first time, we report population sampling from across the entire range of distribution covering the Iberian Peninsula and Morocco. In total, 455 samples were collected from 59 populations. Plastid DNA sequences of matK and ndhF were generated alongside 11 microsatellite loci to permit comparison between plastid and nuclear lineage histories. The plastid DNA phylogenetic tree was highly congruent with previous molecular studies and supported the recognition of these two lineages of hoop-petticoat daffodils as separate sections. Assignment of samples to sections sometimes differed between plastid DNA and (nuclear) microsatellite data. In these cases, the taxa had previously been the focus of dissent in taxonomic placement based on morphology. These discrepancies could be explained by hybridization and introgression among the two lineages during the evolution of hoop-petticoat daffodils, and shows that placement of species in sections is dependent on the source of data used. This study underlines the complex evolutionary history of Narcissus and highlights the discrepancies between floral morphology and phylogeny, which provides a continuing challenge for the systematics of Narcissus.

scholarly journals Tuber Fulgens Quél. A New Record for Turkish Truffles

2020 ◽  
Vol 8 (11) ◽  
pp. 2472-2475
Author(s):  
Ilgaz Akata ◽  
Mustafa Sevindik ◽  
Ergin Şahin
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Large Subunit ◽  
Morphological Data ◽  
Lsu Rdna ◽  
High Sequence Similarity ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
History Of ◽  
First Time

Tuber samples were collected from Kırklareli province on the 10th of August 2020 and they are identified by implementing both traditional methods and molecular phylogenetic analysis using the rDNA sequences including Internal Transcribed Spacer (ITS) and 28S Ribosomal Large Subunit (LSU) regions. By taking into account the high sequence similarity between the collected samples (ANK Akata 7351) and the truffle species Tuber fulgens Quél. the collected specimen was regarded as T. fulgens and the morphological data also consolidated this finding. As a result, T. fulgens was reported for the first time from Turkey. A short description of the newly reported species is given along with its macro and microphotographs, and spore images taken by a scanning electron microscope (SEM). Additionally, ITS and LSU rDNA based evolutionary history of the specimen is provided with phylogenetic trees.

scholarly journals Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae

2004 ◽  
Vol 359 (1450) ◽  
pp. 1495-1508 ◽  
Author(s):  
J. E. Richardson ◽  
L. W. Chatrou ◽  
J. B. Mols ◽  
R. H. J. Erkens ◽  
M. D. Pirie
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Plastid Dna ◽  
Distribution Patterns ◽  
Historical Biogeography ◽  
Rate Heterogeneity ◽  
Long Distance ◽  
Fossil Calibration ◽  
Dispersal Capability

Annonaceae are a pantropically distributed family found predominantly in rainforests, so they are megathermal taxa, whereas Rhamnaceae are a cosmopolitan family that tend to be found in xeric regions and may be classified as mesothermal. Phylogenetic analyses of these families are presented based on rbcL and trn L–F plastid DNA sequences. Likelihood ratio tests revealed rate heterogeneity in both phylogenetic trees and they were therefore made ultrametric using non–parametric rate smoothing and penalized likelihood. Divergence times were then estimated using fossil calibration points. The historical biogeography of these families that are species rich in different biomes is discussed and compared with other published reconstructions. Rhamnaceae and most lineages within Annonaceae are too young to have had their distribution patterns influenced by break–up of previously connected Gondwanan landmasses. Contrasts in the degree of geographical structure between these two families may be explained by differences in age and dispersal capability. In both groups, long–distance dispersal appears to have played a more significant role in establishing modern patterns than had previously been assumed. Both families also contain examples of recent diversification of species–rich lineages. An understanding of the processes responsible for shaping the distribution patterns of these families has contributed to our understanding of the historical assembly of the biomes that they occupy.

scholarly journals Phylogeny of the Labeoninae (Teleostei, Cypriniformes) based on nuclear DNA sequences and implications on character evolution and biogeography

2012 ◽  
Vol 58 (6) ◽  
pp. 837-850 ◽  
Author(s):  
Lanping Zheng ◽  
Junxing Yang ◽  
Xiaoyong Chen
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Morphological Characters ◽  
Character Evolution ◽  
Lower Lip ◽  
Molecular Phylogenetic Tree ◽  
Systematic Exploration ◽  
Molecular Phylogenetic ◽  
History Of

Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals (representing 24 genera and 73 species) of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oroman-dibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine , a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia.

scholarly journals Hundreds of nuclear and plastid loci yield insights into orchid relationships

2020 ◽  
Author(s):  
Oscar Alejandro Pérez-Escobar ◽  
Steven Dodsworth ◽  
Diego Bogarín ◽  
Sidonie Bellot ◽  
Juan A. Balbuena ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Gene Trees ◽  
Deep Time ◽  
Plastid Genomes ◽  
Phylogenetic Informativeness ◽  
History Of ◽  
Phylogenetic Framework

ABSTRACTPremise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

scholarly journals An integrative monograph of Carex section Schoenoxiphium (Cyperaceae)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11336
Author(s):  
Modesto Luceño ◽  
Tamara Villaverde ◽  
José Ignacio Márquez-Corro ◽  
Rogelio Sánchez-Villegas ◽  
Enrique Maguilla ◽  
...  
Keyword(s):  
Plastid Dna ◽  
Eastern Africa ◽  
Herbarium Specimens ◽  
Distribution Maps ◽  
Distinct Genus ◽  
Biogeographic Region ◽  
Center Of Diversity ◽  
History Of ◽  
Nomen Novum ◽  
First Time

Carex section Schoenoxiphium (Cariceae, Cyperaceae) is endemic to the Afrotropical biogeographic region and is mainly distributed in southern and eastern Africa, with its center of diversity in eastern South Africa. The taxon was formerly recognized as a distinct genus and has a long history of taxonomic controversy. It has also an important morphological and molecular background in particular dealing with the complexity of its inflorescence and the phylogenetic relationships of its species. We here present a fully updated and integrative monograph of Carex section Schoenoxiphium based on morphological, molecular and cytogenetic data. A total of 1,017 herbarium specimens were examined and the majority of the species were studied in the field. Previous molecular phylogenies based on Sanger-sequencing of four nuclear and plastid DNA regions and RAD-seq were expanded. For the first time, chromosome numbers were obtained, with cytogenetic counts on 44 populations from 15 species and one hybrid. Our taxonomic treatment recognizes 21 species, one of them herein newly described (C. gordon-grayae). Our results agree with previous molecular works that have found five main lineages in Schoenoxiphium. We provide detailed morphological descriptions, distribution maps and analytical drawings of all accepted species in section Schoenoxiphium, an identification key, and a thorough nomenclatural survey including 19 new typifications and one nomen novum.

scholarly journals SARS-CoV-2 Infection: New Molecular, Phylogenetic, and Pathogenetic Insights. Efficacy of Current Vaccines and the Potential Risk of Variants

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1687 ◽  
Author(s):  
John Charles Rotondo ◽  
Fernanda Martini ◽  
Martina Maritati ◽  
Chiara Mazziotta ◽  
Giulia Di Mauro ◽  
...  
Keyword(s):  
Viral Vector ◽  
Current Knowledge ◽  
Vaccination Campaign ◽  
Positive Effects ◽  
Molecular Phylogenetic ◽  
History Of ◽  
One Year ◽  
Novel Coronavirus ◽  
The Impact ◽  
First Time

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly discovered coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic. COVID-19 has rapidly become a public health emergency of international concern. Although remarkable scientific achievements have been reached since the beginning of the pandemic, the knowledge behind this novel coronavirus, in terms of molecular and pathogenic characteristics and zoonotic potential, is still relatively limited. Today, there is a vaccine, or rather several vaccines, which, for the first time in the history of highly contagious infectious diseases that have plagued mankind, has been manufactured in just one year. Currently, four vaccines are licensed by regulatory agencies, and they use RNA or viral vector technologies. The positive effects of the vaccination campaign are being felt in many parts of the world, but the disappearance of this new infection is still far from being a reality, as it is also threatened by the presence of novel SARS-CoV-2 variants that could undermine the effectiveness of the vaccine, hampering the immunization control efforts. Indeed, the current findings indicate that SARS-CoV-2 is adapting to transmission in humans more efficiently, while further divergence from the initial archetype should be considered. In this review, we aimed to provide a collection of the current knowledge regarding the molecular, phylogenetic, and pathogenetic insights into SARS-CoV-2. The most recent findings obtained with respect to the impact of novel emerging SARS-CoV-2 variants as well as the development and implementation of vaccines are highlighted.

First description of monogenean parasites in Lake Tanganyika: the cichlid Simochromis diagramma (Teleostei, Cichlidae) harbours a high diversity of Gyrodactylus species (Platyhelminthes, Monogenea)

Parasitology ◽  
2010 ◽  
Vol 138 (3) ◽  
pp. 364-380 ◽  
Author(s):  
MAARTEN P. M. VANHOVE ◽  
JOS SNOEKS ◽  
FILIP A. M. VOLCKAERT ◽  
TINE HUYSE
Keyword(s):  
Dna Sequences ◽  
Host Species ◽  
Lake Tanganyika ◽  
Cichlid Fish ◽  
Copulatory Organ ◽  
Fish Parasites ◽  
Nuclear Ribosomal Dna ◽  
Single Host ◽  
History Of ◽  
First Time

SUMMARYLake Tanganyika harbours the most diverse endemic cichlid fish assemblage of Africa, but its monogenean fish parasites have not been investigated. Here we report, for the first time, on the Gyrodactylus parasites in this hotspot of fish biodiversity. Haptor morphometrics and nuclear ribosomal DNA sequences revealed 3 new species on Zambian Simochromis diagramma: Gyrodactylus sturmbaueri n. sp., G. thysi n. sp. and G. zimbae n. sp. Their distinct morphology and strong genetic differentiation suggest that they belong to distant lineages within the genus Gyrodactylus, and phylogenetic reconstructions suggest affinities with other genera of gyrodactylids. Additional U-shaped haptoral plates in G. thysi n. sp. and a second large spine-like structure in the male copulatory organ of G. zimbae seem to represent new features for the genus. Such large diversity on a single host species can probably be explained by host-switching events during the course of evolution, in agreement with the generally accepted concept that ecological transfer is an important aspect of gyrodactylid speciation. Additional parasitological surveys on other host species, covering a broader phylogenetic and geographical range, should clarify the evolutionary history of Gyrodactylidae on cichlids in the African Great Lake and other parts of Africa.

scholarly journals Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences

Biology ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 9 ◽  
Author(s):  
Huyen-Trang Vu ◽  
Quoc-Luan Vu ◽  
Thanh-Diem Nguyen ◽  
Ngan Tran ◽  
Thanh-Cong Nguyen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Species Discrimination ◽  
Nucleotide Polymorphism ◽  
Wild Fauna ◽  
Amplification Rate ◽  
Leaf Coloration ◽  
Bayesian Inference Method ◽  
Over Exploitation ◽  
First Time

Paphiopedilum is among the most popular ornamental orchid genera due to its unique slipper flowers and attractive leaf coloration. Most of the Paphiopedilum species are in critical danger due to over-exploitation. They were listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents their being traded across borders. While most Paphiopedilum species are distinctive, owing to their respective flowers, their vegetative features are more similar and undistinguished. Hence, the conservation of these species is challenging, as most traded specimins are immature and non-flowered. An urgent need exists for effective identification methods to prevent further illegal trading of Paphiopedilum species. DNA barcoding is a rapid and sensitive method for species identification, at any developmental stage, using short DNA sequences. In this study, eight loci, i.e., ITS, LEAFY, ACO, matK, trnL, rpoB, rpoC1, and trnH-psbA, were screened for potential barcode sequences on the Vietnamese Paphiopedilum species. In total, 17 out of 22 Paphiopedilum species were well identified. The studied DNA sequences were deposited to GenBank, in which Paphiopedilum dalatense accessions were introduced for the first time. ACO, LEAFY, and trnH-psbA were limited in amplification rate for Paphiopedilum. ITS was the best single barcode. Single ITS could be used along with nucleotide polymorphism characteristics for species discrimination. The combination of ITS + matK was the most efficient identification barcode for Vietnamese Paphiopedilum species. This barcode also succeeded in recognizing misidentified or wrongly-named traded samples. Different bioinformatics programs and algorithms for establishing phylogenetic trees were also compared in the study to propose quick, simple, and effective tools for practical use. It was proved that both the Bayesian Inference method in the MRBAYES program and the neighbor-joining method in the MEGA software met the criteria. Our study provides a barcoding database of Vietnamese Paphiopedilum which may significantly contribute to the control and conservation of these valuable species.

scholarly journals Mitochondrial DNA Sequence Phylogeny of Daucus

2020 ◽  
Vol 45 (2) ◽  
pp. 403-408 ◽  
Author(s):  
David M. Spooner ◽  
Holly Ruess ◽  
Philipp Simon ◽  
Douglas Senalik
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Plastid Dna ◽  
Nuclear Data ◽  
Bootstrap Support ◽  
Illumina Hiseq ◽  
Data Set ◽  
Closely Related Species ◽  
Mitochondrial Sequences

Abstract—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.

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