Molecular evidence for hybridization in the aquatic plant Limosella on sub-Antarctic Marion Island

Abstract DNA sequence data have become a crucial tool in assessing the relationship between morphological variation and genetic and taxonomic groups, including in the Antarctic biota. Morphologically distinct populations of submersed aquatic vascular plants were observed on sub-Antarctic Marion Island, potentially representing the two species of such plants listed in the island's flora, Limosella australis R.Br. (Scrophulariaceae) and Ranunculus moseleyi Hook.f. (Ranunculaceae). To confirm their taxonomic identity, we sequenced a nuclear locus (internal transcribed spacer; ITS) and two plastid loci (trnL-trnF, rps16) from three specimens collected on Marion Island and compared the sequences with those in public sequence databases. For all three loci, sequences from the Marion Island specimens were nearly identical despite morphological dissimilarity, and phylogenetic analyses resolved them to a position in Limosella. In phylogenetic trees and comparisons of species-specific sequence polymorphisms, the Marion Island specimens were closest to a clade comprising Limosella aquatica L., L. curdieana F.Muell. and L. major Diels for ITS and closest to L. australis for the plastid loci. Cytonuclear discordance suggests a history of hybridization or introgression, which may have consequences for morphological variability and ecological adaptation.

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A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida)

PeerJ ◽

10.7717/peerj.3354 ◽

2017 ◽

Vol 5 ◽

pp. e3354 ◽

Cited By ~ 15

Author(s):

Timur G. Simdyanov ◽

Laure Guillou ◽

Andrei Y. Diakin ◽

Kirill V. Mikhailov ◽

Joseph Schrével ◽

...

Keyword(s):

Electron Microscopy ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Wide Distribution ◽

Phylogenetic Study ◽

Molecular Evidence ◽

Molecular Phylogenetic ◽

Phylogenetic Lineages

Background Gregarines are a group of early branching Apicomplexa parasitizing invertebrate animals. Despite their wide distribution and relevance to the understanding the phylogenesis of apicomplexans, gregarines remain understudied: light microscopy data are insufficient for classification, and electron microscopy and molecular data are fragmentary and overlap only partially. Methods Scanning and transmission electron microscopy, PCR, DNA cloning and sequencing (Sanger and NGS), molecular phylogenetic analyses using ribosomal RNA genes (18S (SSU), 5.8S, and 28S (LSU) ribosomal DNAs (rDNAs)). Results and Discussion We present the results of an ultrastructural and molecular phylogenetic study on the marine gregarine Ancora sagittata from the polychaete Capitella capitata followed by evolutionary and taxonomic synthesis of the morphological and molecular phylogenetic evidence on eugregarines. The ultrastructure of Ancora sagittata generally corresponds to that of other eugregarines, but reveals some differences in epicytic folds (crests) and attachment apparatus to gregarines in the family Lecudinidae, where Ancora sagittata has been classified. Molecular phylogenetic trees based on SSU (18S) rDNA reveal several robust clades (superfamilies) of eugregarines, including Ancoroidea superfam. nov., which comprises two families (Ancoridae fam. nov. and Polyplicariidae) and branches separately from the Lecudinidae; thus, all representatives of Ancoroidea are here officially removed from the Lecudinidae. Analysis of sequence data also points to possible cryptic species within Ancora sagittata and the inclusion of numerous environmental sequences from anoxic habitats within the Ancoroidea. LSU (28S) rDNA phylogenies, unlike the analysis of SSU rDNA alone, recover a well-supported monophyly of the gregarines involved (eugregarines), although this conclusion is currently limited by sparse taxon sampling and the presence of fast-evolving sequences in some species. Comparative morphological analyses of gregarine teguments and attachment organelles lead us to revise their terminology. The terms “longitudinal folds” and “mucron” are restricted to archigregarines, whereas the terms “epicystic crests” and “epimerite” are proposed to describe the candidate synapomorphies of eugregarines, which, consequently, are considered as a monophyletic group. Abolishing the suborders Aseptata and Septata, incorporating neogregarines into the Eugregarinida, and treating the major molecular phylogenetic lineages of eugregarines as superfamilies appear as the best way of reconciling recent morphological and molecular evidence. Accordingly, the diagnosis of the order Eugregarinida Léger, 1900 is updated.

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A species-specific satellite DNA from the entomopathogenic nematode Heterorhabditis indicus

Genome ◽

10.1139/g98-005 ◽

1998 ◽

Vol 41 (2) ◽

pp. 148-153 ◽

Cited By ~ 8

Author(s):

Monique Abadon ◽

Eric Grenier ◽

Christian Laumond ◽

Pierre Abad

Keyword(s):

Dna Sequence ◽

Satellite Dna ◽

Tandem Repeats ◽

Sequence Data ◽

Entomopathogenic Nematode ◽

Consensus Sequence ◽

Repeated Sequence ◽

Nucleotide Sequence Analysis ◽

Specific Sequence ◽

Species Specific

An AluI satellite DNA family has been cloned from the entomopathogenic nematode Heterorhabditis indicus. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 45% of the H. indicus genome. The consensus sequence is 174 nucleotides long and has an A + T content of 56%, with the presence of direct and inverted repeat clusters. DNA sequence data reveal that monomers are quite homogeneous. Such homogeneity suggests that some mechanism is acting to maintain the homogeneity of this satellite DNA, despite its abundance, or that this repeated sequence could have appeared recently in the genome of H. indicus. Hybridization analysis of genomic DNAs from different Heterorhabditis species shows that this satellite DNA sequence is specific to the H. indicus genome. Considering the species specificity and the high copy number of this AluI satellite DNA sequence, it could provide a rapid and powerful tool for identifying H. indicus strains.Key words: AluI repeated DNA, tandem repeats, species-specific sequence, nucleotide sequence analysis.

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A revision of the planthopper genus Chionomus Fennah (Hemiptera: Fulgoroidea: Delphacidae)

Zootaxa ◽

10.11646/zootaxa.4811.1.1 ◽

2020 ◽

Vol 4811 (1) ◽

pp. 1-63

Author(s):

KATHRYN M. WEGLARZ ◽

CHARLES R BARTLETT

Keyword(s):

Mixed Model ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Molecular Evidence ◽

Additional Species ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Original Definition ◽

Definition Of

The planthopper genus Chionomus Fennah, 1971 (Hemiptera: Fulgoroidea: Delphacidae) currently includes three Neotropical species, removed from the polyphyletic genus Delphacodes Fieber, 1866. Morphological and molecular evidence further redefine Chionomus to include ten additional species (eight species removed from Delphacodes, two described as new, viz. Chionomus dolonus n. sp. and C. herkos n. sp.), with another four species synonymized. Phylogenetic analyses of morphological and molecular sequence data of the mitochondrial gene Cytochrome Oxidase I provide support for the monophyly of Chionomus. We use a mixed model Bayesian optimality criterion to define phylogenetic relationships among Chionomus and support paraphyly of the original definition of Chionomus (with respect to Delphacodes) and monophyly of the revised genus.

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Evolution of pollination syndromes and corolla symmetry in Balsaminaceae reconstructed using phylogenetic comparative analyses

Annals of Botany ◽

10.1093/aob/mcaa184 ◽

2020 ◽

Author(s):

Saroj Ruchisansakun ◽

Arne Mertens ◽

Steven B Janssens ◽

Erik F Smets ◽

Timotheüs van der Niet

Keyword(s):

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Plastid Dna ◽

Pollination Syndrome ◽

Pollination Syndromes ◽

Bee Pollination ◽

Floral Symmetry ◽

Considerable Uncertainty ◽

Pollination Systems

Abstract Background and Aims Floral diversity as a result of plant–pollinator interactions can evolve by two distinct processes: shifts between pollination systems or divergent use of the same pollinator. Although both are pollinator driven, the mode, relative importance and interdependence of these different processes are rarely studied simultaneously. Here we apply a phylogenetic approach using the Balsaminaceae (including the species-rich genus Impatiens) to simultaneously quantify shifts in pollination syndromes (as inferred from the shape and colour of the perianth), as well as divergent use of the same pollinator (inferred from corolla symmetry). Methods For 282 species we coded pollination syndromes based on associations between floral traits and known pollination systems, and assessed corolla symmetry. The evolution of these traits was reconstructed using parsimony- and model-based approaches, using phylogenetic trees derived from phylogenetic analyses of nuclear ribosomal and plastid DNA sequence data. Key Results A total of 71 % of studied species have a bee pollination syndrome, 22 % a bimodal syndrome (Lepidoptera and bees), 3 % a bird pollination syndrome and 5 % a syndrome of autogamy, while 19 % of species have an asymmetrical corolla. Although floral symmetry and pollination syndromes are both evolutionarily labile, the latter shifts more frequently. Shifts in floral symmetry occurred mainly in the direction towards asymmetry, but there was considerable uncertainty in the pattern of shift direction for pollination syndrome. Shifts towards asymmetrical flowers were associated with a bee pollination syndrome. Conclusion Floral evolution in Impatiens has occurred through both pollination syndrome shifts and divergent use of the same pollinator. Although the former appears more frequent, the latter is likely to be underestimated. Shifts in floral symmetry and pollination syndromes depend on each other but also partly on the region in which these shifts take place, suggesting that the occurrence of pollinator-driven evolution may be determined by the availability of pollinator species at large geographical scales.

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Sequence variability in two mitochondrial DNA regions and internal transcribed spacer among three cestodes infecting animals and humans from China

Journal of Helminthology ◽

10.1017/s0022149x11000319 ◽

2011 ◽

Vol 86 (2) ◽

pp. 245-251 ◽

Cited By ~ 37

Author(s):

R.S. Dai ◽

G.H. Liu ◽

H.Q. Song ◽

R.Q. Lin ◽

Z.G. Yuan ◽

...

Keyword(s):

Mitochondrial Dna ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Phylogenetic Analyses ◽

The Other ◽

Sequence Variability ◽

Taenia Hydatigena ◽

Specific Sequence ◽

5.8S Rdna ◽

Rdna Sequences

AbstractSequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochromecoxidase subunit 1 (cox1) and NADH dehydrogenase subunit 4 (nad4), and internal transcribed spacer (ITS) of rDNA among and within three cestodes,Spirometra erinaceieuropaei,Taenia multicepsandTaenia hydatigena, from different geographical origins in China was examined. A portion of thecox1 (pcox1),nad4 genes (pnad4) and the ITS (ITS1+5.8S rDNA+ITS2) were amplified separately from individual cestodes by polymerase chain reaction (PCR). Representative amplicons were subjected to sequencing in order to estimate sequence variability. While the intra-specific sequence variations within each of the tapeworm species were 0–0.7% for pcox1, 0–1.7% for pnad4 and 0.1–3.6% for ITS, the inter-specific sequence differences were significantly higher, being 12.1–17.6%, 18.7–26.2% and 31–75.5% for pcox1, pnad4 and ITS, respectively. Phylogenetic analyses based on the pcox1 sequence data revealed thatT. multicepsandT. hydatigenawere more closely related to the other members of theTaeniagenus, andS. erinaceieuropaeiwas more closely related to the other members of theSpirometragenus. These findings demonstrated clearly the usefulness of mtDNA and rDNA sequences for population genetic studies of these cestodes of socio-economic importance.

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On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology

Frontiers in Plant Science ◽

10.3389/fpls.2021.743643 ◽

2021 ◽

Vol 12 ◽

Author(s):

Na Su ◽

Bin-bin Liu ◽

Jun-ru Wang ◽

Ru-chang Tong ◽

Chen Ren ◽

...

Keyword(s):

Species Delimitation ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Reconstruction ◽

Phylogenetic Network ◽

Single Copy ◽

Morphological Evidence ◽

Molecular Evidence ◽

Variable Regions ◽

Dna Sequence Data

The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.

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A rare case of equine Haemotropic Mycoplasma infection in Nigeria

Nigerian Veterinary Journal ◽

10.4314/nvj.v41i3.8 ◽

2021 ◽

Vol 41 (3) ◽

pp. 274-286

Author(s):

A.N Happi ◽

P.E Oluniyi

Keyword(s):

16S Rrna ◽

Bacterial Infections ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Clinical Findings ◽

Epidemiological Surveillance ◽

Response To Treatment ◽

Molecular Evidence ◽

Rrna Gene ◽

16S Rrna Sequence

Equine haemotropic mycoplasmosis (EHM) is a condition rarely reported worldwide. A horse presented with unspecific clinical findings and non-response to treatment to the common and endemic haemoparasitic and bacterial infections, warranted a thorough molecular investigation of suspected haemoparasitic infection given the fluctuating parasitaemia and the low sensitivity and specificity of Light Microscopy (LM) detection of haemoparasitic infections. Blood collected from an adult horse, domiciled at the University of Ibadan Veterinary Teaching Hospital, Ibadan, Nigeria was screened by LM and PCR techniques for haemo-parasites. The 16S rRNA gene of pan-Hemoplasma spp was targeted amplified and sequenced using Sanger automatic sequencing techniques. This case shows the very first molecular evidence of EHM in Africa and Nigeria, and the third case in the World. Microscopic examination of the horse’s blood smear presented with signs of lethargy, inactivity, anorexia and moderate emaciation, showed numerous coccoid-shaped epierythrocytic parasites. Subsequent 16S rRNA sequence data and phylogenetic analyses confirmed the presence of a haemotropic mycoplasma (‘Candidatus M. haemocervae’–like) in the horse. The hemoplasma sequence obtained falls in the same clade with some Candidatus Mycoplasma haemocervae sequences with which it shared more than 98.7% homology. This finding suggests that horses in this geographical region may also be suffering from EHM and calls for the need of epidemiological surveillance of equine hemoplasmosis with emphasis on their clinical, economic, performance and zoonotic implications in the sub-region. Keywords: Nigeria, Horse, Haemotropic mycoplasma, ‘Candidatus M. haemocervae’–like

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Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

10.7287/peerj.preprints.1106v1 ◽

2015 ◽

Author(s):

Jennifer Fouquier ◽

Jai R Rideout ◽

Evan Bolyen ◽

John H Chase ◽

Arron Shiffer ◽

...

Keyword(s):

Phylogenetic Tree ◽

Genetic Marker ◽

Phylogenetic Trees ◽

Phylogenetic Diversity ◽

Sequence Data ◽

Fungal Species ◽

Bioinformatics Tool ◽

Hybrid Gene ◽

Fungal Database ◽

Taxonomic Groups

Ghost-tree is a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach uses one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families) as a “foundation” phylogeny. A second, more rapidly evolving genetic marker is then used to build “extension” phylogenies for more closely related organisms (e.g., fungal species or strains) that are then grafted on to the foundation tree by mapping taxonomic names. We apply ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. The result is a phylogenetic tree, compatible with the commonly used UNITE fungal database, that supports phylogenetic diversity analysis (e.g., UniFrac) of fungal communities profiled using ITS markers. Availability: ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree.

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Cymbidium yunnanensis: a new orchid species (Orchidaceae; Epidendroideae) from China based on morphological and molecular evidence

Phytotaxa ◽

10.11646/phytotaxa.387.2.7 ◽

2019 ◽

Vol 387 (2) ◽

pp. 149-157 ◽

Cited By ~ 5

Author(s):

GUO-QIANG ZHANG ◽

GUI-ZHEN CHEN ◽

LI-JUN CHEN ◽

SI-REN LAN

Keyword(s):

New Species ◽

Dna Sequence ◽

Yunnan Province ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Evidence ◽

Orchid Species ◽

Molecular Analyses ◽

Dna Sequence Data ◽

A New Species

A new orchid species, Cymbidium yunnanensis (Orchidaceae; Epidendroideae; Cymbidieae), from Yunnan Province, China, is described and illustrated. Based on morphological and molecular analyses, we demonstrate that this new species is similar to C. floribundum, but it differs in its smaller size, leaves 5–15 cm, shorter scape, white flowers with pale purplish markings on its sepals and petals, lip with purplish red blotch, petals narrowly falcate oblong and lip midlobe nearly round with column foot 1.5–2.0 mm long. Phylogenetic analyses based on nuclear ribosomal ITS and plastid (matK, rbcL) DNA sequence data support C. yunnanensis as a new species.

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Reappraisal of Immotthia in Dictyosporiaceae, Pleosporales: Introducing Immotthia bambusae sp. nov. and Pseudocyclothyriella clematidis comb. et gen. nov. Based on Morphology and Phylogeny

Frontiers in Microbiology ◽

10.3389/fmicb.2021.656235 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hong-Bo Jiang ◽

Rajesh Jeewon ◽

Samantha C. Karunarathna ◽

Chayanard Phukhamsakda ◽

Mingkwan Doilom ◽

...

Keyword(s):

Dna Sequence ◽

Phylogenetic Trees ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Single Species ◽

Type Specimen ◽

Morphological Identification ◽

Ongoing Research ◽

Dna Sequence Data

Immotthia is a poorly known genus, and currently, no DNA sequence data are available to ascertain its proper phylogenetic placement and evolutionary relationships with other bitunicate fungi. To date, there are only two species accepted in the genus. During our ongoing research study of bambusicolous fungi in southwest China and Thailand, a fungus associated with stromata of Hypoxylon sp. was found on dead bamboo culms in Loei Province, Thailand. Preliminary morphological identification revealed that the fungal collection belongs to Immotthia. A novel species, Immotthia bambusae, is introduced herein based on a comparison of morphological characteristics with the type specimen of I. hypoxylon (≡ Amphisphaeria hypoxylon Ellis and Everh.), a synonym of I. atrograna (Cooke and Ellis) M. E. Barr. Phylogenetic analyses of a concatenated ITS, LSU, SSU, and TEF1-α DNA sequence matrix showed that Immotthia belongs to Dictyosporiaceae, Pleosporales. Despite I. bambusae strains constituting a supported subclade, they are nested with the genus Pseudocoleophoma. Pseudocoleophoma clematidis is morphologically different from all other Pseudocoleophoma species, while its conidial characteristics are similar to Cyclothyriella. Multigene phylogenetic analyses showed that P. clematidis formed a clade basal to Immotthia, separated from Pseudocoleophoma with strong statistical support. Therefore, we introduce a monotypic genus, Pseudocyclothyriella Phukhams. and Phookamsak, gen. nov. to accommodate the single species, Pseudocyclothyriella clematidis (Phukhams. and K. D. Hyde) Phukhams. and Phookamsak, comb. nov. Detailed descriptions, color micrographs, and phylogenetic trees to show the placement of the new taxa are provided. In addition, an updated taxonomic treatment of the genera Immotthia and Pseudocyclothyriella is also provided based on the study of the type materials and phylogeny generated from DNA sequence data.

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