scholarly journals Plastome variation and phylogeny of Taxillus (Loranthaceae)

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256345
Author(s):  
Huei-Jiun Su ◽  
Shu-ling Liang ◽  
Daniel L. Nickrent
Keyword(s):  
Nadh Dehydrogenase ◽  
General Pattern ◽  
Trna Genes ◽  
Dna Barcodes ◽  
Variable Regions ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Difficult Genus ◽  
Molecular Phylogenetic ◽  
Mitochondrial Rdna

Several molecular phylogenetic studies of the mistletoe family Loranthaceae have been published such that now the general pattern of relationships among the genera and their biogeographic histories are understood. Less is known about species relationships in the larger (> 10 species) genera. This study examines the taxonomically difficult genus Taxillus composed of 35–40 Asian species. The goal was to explore the genetic diversity present in Taxillus plastomes, locate genetically variable hotspots, and test these for their utility as potential DNA barcodes. Using genome skimming, complete plastomes, as well as nuclear and mitochondrial rDNA sequences, were newly generated for eight species. The plastome sequences were used in conjunction with seven publicly available Taxillus sequences and three sequences of Scurrula, a close generic relative. The Taxillus plastomes ranged from 121 to 123 kbp and encoded 90–93 plastid genes. In addition to all of the NADH dehydrogenase complex genes, four ribosomal genes, infA and four intron-containing tRNA genes were lost or pseudogenized in all of the Taxillus and Scurrula plastomes. The topologies of the plastome, mitochondrial rDNA and nuclear rDNA trees were generally congruent, though with discordance at the position of T. chinensis. Several variable regions in the plastomes were identified that have sufficient numbers of parsimony informative sites as to recover the major clades seen in the complete plastome tree. Instead of generating complete plastome sequences, our study showed that accD alone or the concatenation of accD and rbcL can be used in future studies to facilitate identification of Taxillus samples and to generate a molecular phylogeny with robust sampling within the genus.

scholarly journals Use of nuclear genes for phylogeny reconstruction in plants

2004 ◽  
Vol 17 (2) ◽  
pp. 145 ◽  
Author(s):  
Randall L. Small ◽  
Richard C. Cronn ◽  
Jonathan F. Wendel
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Nuclear Genes ◽  
Universal Primers ◽  
Plant Systematics ◽  
Dna Sequence Data ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Orthologous Loci

Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies.

Molecular phylogenetic studies on the Parmotrema reticulatum (syn. Rimelia reticulata) complex, including the confirmation of P. pseudoreticulatum as a distinct species

2005 ◽  
Vol 37 (1) ◽  
pp. 55-65 ◽  
Author(s):  
Pradeep K. DIVAKAR ◽  
Oscar BLANCO ◽  
David L. HAWKSWORTH ◽  
Ana CRESPO
Keyword(s):  
South Africa ◽  
Western Europe ◽  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Ssu Rdna ◽  
Monophyletic Clade ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Nuclear Its

Molecular phylogenetic analyses based on nuclear ITS rDNA and mitochondrial SSU rDNA sequences from 32 specimens representing Parmotrema pseudoreticulatum, P. reticulatum and P. clavuliferum from Africa, Asia, Australia, and Europe are reported. Samples from western Europe and South Africa formed an independent monophyletic group, which belongs to P. pseudoreticulatum, a species not accepted by some recent authors, that has only been reported from Portugal, Spain and Morocco. In contrast, P. reticulatum and P. clavuliferum, both widely distributed taxa, formed a monophyletic clade, supporting the synonymy already proposed on the basis of morphological features.

scholarly journals Morphological re-assessment of the Boodlea composita - Phyllodictyon anastomosans species complex (Siphonocladales: Chlorophyta)

2007 ◽  
Vol 20 (2) ◽  
pp. 161 ◽  
Author(s):  
Frederik Leliaert ◽  
Eric Coppejans
Keyword(s):  
Species Complex ◽  
Cell Types ◽  
Species Boundaries ◽  
Growth Forms ◽  
True Nature ◽  
Taxonomic Level ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Cell Dimensions ◽  
Molecular Phylogenetic

Boodlea composita (Harvey) F. Brand and Phyllodictyon anastomosans (Harvey) Kraft & M.J. Wynne, two widespread tropical siphonocladalean green algae, have had a long and confusing history because of the vague taxonomic boundaries between the two species. Molecular phylogenetic studies on the basis of nuclear-encoded rDNA sequences have resolved these indistinct species boundaries and suggest these taxa are part of a species complex. Detailed morphological investigations in combination with field and culture observations show that the concept of traditionally recognised taxa in this species complex is clouded by an ecologically induced phenotypic plasticity and developmental variability. Examination of a large number of specimens of B. composita, P. anastomosans and morphologically allied taxa including Boodlea siamensis Reinbold, Boodlea montagnei (Harvey ex J.E. Gray) Egerod, Nereodictyon imitans Gerloff and Struveopsis siamensis (Egerod) P. C. Silva, worldwide, including types, shows a wide morphological variety. We recognise seven more or less distinct morphological entities based on differences in thallus architectures, branching systems, cell dimensions and tenacular cell types. Awaiting the recovery of the true nature of the defined entities in this species complex (different species or growth forms of the same species), they are referred to as morphotypes, i.e. making no assumptions as to which taxonomic level they best apply.

scholarly journals A molecular perspective on generic concepts in the Hypotrachyna clade (Parmeliaceae, Ascomycota)

Phytotaxa ◽  
2013 ◽  
Vol 132 (1) ◽  
pp. 21 ◽  
Author(s):  
PRADEEP K. DIVAKAR ◽  
ANA CRESPO ◽  
JANO NÚÑEZ-ZAPATA ◽  
ADAM FLAKUS ◽  
HARRIE J.M. SIPMAN ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
New Combinations ◽  
Generic Delimitation ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Alternative Hypotheses ◽  
Nuclear Its

Recently, molecular phylogenetic studies have revolutionized the generic concepts in Parmeliaceae and in lichen forming fungi in general. In the present study, the generic delimitation in the Hypotrachyna clade is revised using a molecular phylogeny of nuclear ITS, LSU and mitochondrial SSU rDNA sequences of 88 hypotrachynoid taxa. Morphological and chemical features are also revised in each group. 118 sequences are newly generated for this study. Our phylogenetic analyses show the polyphyly of Hypotrachyna as currently circumscribed which falls into four well-supported and one unsupported clade. Cetrariastrum, Everniastrum and Parmelinopsis are nested within Hypotrachyna s. lat., Parmelinopsis being also polyphyletic and nested in one of the Hypotrachyna clades. Cetrariastrum is monophyletic but clustered within Everniastrum. Two alternative hypotheses tests significantly rejected the monophyly of these three genera. As a consequence, the genera Cetrariastrum, Everniastrum, and Parmelinopsis are reduced to synonymy with Hypotrachyna. Furthermore, we here propose an alternative classification to recognize the well-supported clades at subgeneric level and leave the remaining species unclassified within the genus. Five new subgenera are proposed: Hypotrachyna subgen. Cetrariastrum, Hypotrachyna subgen. Everniastrum, Hypotrachyna subgen. Longilobae, Hypotrachyna subgen. Parmelinopsis, and Hypotrachyna subgen. Sinuosae. Forty-nine new combinations are proposed.

Molecular phylogenetic studies of Turkish boletes with emphasis on some recently described species

Nova Hedwigia ◽  
2020 ◽  
Vol 110 (1) ◽  
pp. 99-129 ◽  
Author(s):  
Fuat Bozok ◽  
Boris Assyov ◽  
Hatıra TaşKın ◽  
Hasan Hüseyin Doğan ◽  
Saadet Büyükalaca
Keyword(s):  
Eastern Mediterranean ◽  
Original Description ◽  
Mediterranean Area ◽  
Morphological Characters ◽  
Its Rdna ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Eastern Mediterranean Area

The paper presents the results of the first molecular phylogenetic assessment of ITS rDNA sequences of members of the family Boletaceae in Turkey. The still little-known species Neoboletus xanthopus and Rubroboletus demonensis are discussed based on Turkish records, which are second after their original description. Data suggest that N. xanthopus may be much more vari- able than currently known, especially what concerns the perceived distinguishing characters from N. erythropus. In addition, first collections of Rubroboletus lupinus s. l. in Turkey are also studied, showing some genetic distinction, seemingly related to the recently communicated from adjacent countries in the Eastern Mediterranean area. An updated key for identification of Turkish and extra-limital European boletes from the former Boletus s. l. is included, based on macroscopic and micro-morphological characters.

Transfer of the Kobresia taxa of the flora of Russia and adjacent countries to the genus Carex (Cyperaceae)

2020 ◽  
pp. 125-129
Author(s):  
D. G. Melnikov ◽  
L. I. Krupkina
Keyword(s):  
International Collaboration ◽  
Morphological Characters ◽  
Published Data ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
New Nomenclatural Combinations

Based on the published data of molecular phylogenetic studies of the tribe Cariceae Dumort. genera (Cyperaceae), obtained by an international collaboration (The Global Carex Group, 2016; et al.), and morphological characters of the genera (Kukkonen, 1990; and others), new nomenclatural combinations and replacement names in the genus Carex L. are published for 11 species, one subspecies and two sections previously included in the genus Kobresia Willd.

Systematics and evolution of Lentibulariaceae: III. Utricularia

2018 ◽  
Author(s):  
Richard W. Jobson ◽  
Paulo C. Baleeiro ◽  
Cástor Guisande
Keyword(s):  
Gene Flow ◽  
Species Diversity ◽  
Population Level ◽  
Oceanic Islands ◽  
Vulnerable Species ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic

Utricularia is a morphologically and ecologically diverse genus currently comprising more than 230 species divided into three subgenera—Polypompholyx, Utricularia, and Bivalvaria—and 35 sections. The genus is distributed worldwide except on the poles and most oceanic islands. The Neotropics has the highest species diversity, followed by Australia. Compared to its sister genera, Utricularia has undergone greater rates of speciation, which are linked to its extreme morphological flexibility that has resulted in the evolution of habitat-specific forms: terrestrial, rheophytic, aquatic, lithophytic, and epiphytic. Molecular phylogenetic studies have resolved relationships for 44% of the species across 80% of the sections. Scant data are available for phylogeography or population-level processes such as gene flow, hybridization, or pollination. Because nearly 90% of the species are endemics, data are urgently needed to determine how to protect vulnerable species and their habitats.

scholarly journals Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

2021 ◽  
Vol 7 (12) ◽  
pp. eabe2741
Author(s):  
Paschalia Kapli ◽  
Paschalis Natsidis ◽  
Daniel J. Leite ◽  
Maximilian Fursman ◽  
Nadia Jeffrie ◽  
...  
Keyword(s):  
Systematic Error ◽  
Tree Reconstruction ◽  
Simulation Experiments ◽  
Animal Evolution ◽  
Phylogenetic Studies ◽  
Branch Lengths ◽  
Molecular Phylogenetic ◽  
Common Ancestors

The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors—inadequate models, short internal branches, faster evolving genes, and unequal branch lengths—coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.

scholarly journals The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ying-ying Ye ◽  
Jing Miao ◽  
Ya-hong Guo ◽  
Li Gong ◽  
Li-hua Jiang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Phylogenetic Studies ◽  
Gc Skew ◽  
Strong Bootstrap Support

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

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