scholarly journals About Notiophilus Duméril, 1806 (Coleoptera, Carabidae): Species delineation and phylogeny using DNA barcodes

2019 ◽  
Vol 66 (1) ◽  
pp. 63-73 ◽  
Author(s):  
Michael J. Raupach ◽  
Karsten Hannig ◽  
Jérome Morinière ◽  
Lars Hendrich
Keyword(s):  
Phylogenetic Analysis ◽  
North America ◽  
Central Europe ◽  
Dna Barcodes ◽  
Species Delineation ◽  
Close Relationship ◽  
Relationship Of

The genus Notiophilus Duméril, 1806 is a distinctive taxon of small, diurnal and morphologically similar beetles exhibiting large eyes and widened second elytral intervals. In this study we analysed the effectiveness of DNA barcodes to discriminate 67 specimens that represent 8 species of Notiophilus from Central Europe. Interspecific K2P distances below 2.2% were found for N.biguttatus (Fabricius, 1779) and N.quadripunctatus Dejean, 1826, whereas intraspecific distances with values > 2.2% were revealed for N.rufipes Curtis, 1829. An additional phylogenetic analysis of all available species revealed a close relationship of N.directus Casey, 1920, N.semistriatus Say, 1823, N.simulator Fall, 1906 and N.sylvaticus Dejean, 1831, possibly indicating a radiation of these species in North America. Low support values of most other nodes, however, do not allow additional phylogenetic conclusions.

scholarly journals Using ITS-rDNA and matK gene nucleotide sequences for identification ginseng species in Panax in Phu Xai Lai Leng, Ky Son, Nghe An

2020 ◽  
Vol 18 (1) ◽  
pp. 75-85
Author(s):  
Vu Dinh Duy ◽  
Tran Thi Viet Thanh ◽  
Phan Ke Loc ◽  
Nguyen Minh Tam ◽  
Nguyen Thi Thanh Huong ◽  
...  
Keyword(s):  
Success Rate ◽  
Genetic Distances ◽  
Its Rdna ◽  
Dna Barcodes ◽  
Phylogenetic Taxonomy ◽  
Panax Species ◽  
Pcr Product ◽  
Matk Gene ◽  
Close Relationship ◽  
Relationship Of

DNA barcoding is a useful tool for species identification using standardized genomic DNA fragments. We used DNA barcodes (ITS-rDNA and matK gene) to explore Panax (32 samples collected from Phu Xai Lai Leng mountain and 19 samples collected from medicinal nursery of TH), and to investigate the phylogenetic taxonomy of Panax. In this study, the PCR success rate for ITS-rDNA and matK region was 100%. The success rate of bidirectional sequencing of PCR product was 100% of ITS-rDNA and matK region with length of 616 bp, 1433 bp, respectively. All 32 samples (Panax TB) of Phu Xai Lai Leng have a close relationship with P. stipuleanatus (MLBS = 99%, BPP = 100%). All 19 samples (Panax TH) of medicinal nursery have a close relationship with P. notoginseng (MLBS = 100%, BPP = 100%). Interspecific genetic distances within and among Panax species was varied from 0.2% to 7.9%, average (4%) (ITS-rDNA gene) and 0.1 to 2.9%, average (1.2%) (matK gene). The genetic relationship of species/gender belonging to the Panax genus showed that they have the same evolutionary origin and discovered that new distributed of P. stipuleanatus in Phu Xai Lai Leng mountain in Vietnam.

scholarly journals Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249537
Author(s):  
Marie Gurke ◽  
Amalia Vidal-Gorosquieta ◽  
Johanna L. A. Pajimans ◽  
Karolina Wȩcek ◽  
Axel Barlow ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Time Frame ◽  
High Similarity ◽  
Close Relationship ◽  
Agricultural Societies ◽  
Time Periods ◽  
Relationship Of ◽  
Insight Into ◽  
Spanish Region

Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia.

scholarly journals Investigation of the red algal parasites Rhodophyllis parasitica sp. nov. and Pterocladiophila hemisphaerica from New Zealand

2021 ◽  
Author(s):  
◽  
Maren Preuss
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Parasite Species ◽  
Nuclear Dna ◽  
Morphological Characteristics ◽  
Close Relationship ◽  
Red Algal ◽  
Different Origins ◽  
Relationship Of ◽  
The Relationship

<p>Red algal parasites are common within red algae and most parasites are closely related to their host. Red algal parasites can switch hosts and their development is unique. Red algal parasites are poorly known in New Zealand. There are only four parasites described in New Zealand and those are based on morphological characteristics. This thesis focuses on the two red algal parasites Rhodophyllis parasitica sp. nov. and Pterocladiophila hemisphaerica from New Zealand. First, development and phylogeny and distribution of an undescribed red algal parasite growing on Rhodophyllis membranacea was investigated. Microscopy, molecular markers (ITS2, cox1, cox2-3 spacer) and phylogenetic analysis, and herbarium sampling were used to address these questions. The parasite, described as Rhodophyllis parasitica sp. nov. shows a close relationship of all genomes to Rhodophyllis membranacea, which suggests that the parasite evolved from its hosts. The parasite is widely distributed throughout New Zealand. The second parasite, Pterocladiophila hemisphaerica was grouped taxonomically, based on morphology, in the order Gracilariales and parasitizes Pterocladia lucida in the order Gelidiales. Molecular marker were used to reveal the relationship of Pterocladiophila hemisphaerica to its host: if the parasite is grouped in the Gracilariales or the Gelidiales; if host switches might have occurred; and if atp8 is present in the parasite. Nuclear DNA (SSU rRNA, LSU rRNA), mitochondrial (cox1) and plastid regions (rbcL-rbcS spacer) from the parasite were sequenced and phylogenetic analysis performed. New primer were designed to amplify atp8 and genetic analysis performed. Pterocladiophila hemisphaerica evolved in the Florideophytes but neither in the Gracilariales or Gelidiales and the parasite possibly switched hosts at least two times, which was shown by three different origins of chloroplast, mitochondria and nuclear DNA. Atp8 in the parasite is present but probably a pseudogene. Rhodophyllis parasitica sp. nov. is the first described red algal parasite species in New Zealand in 55 years and Pterocladiophila hemisphaerica is the first parasite with organelles and nuclei with different histories of origin.</p>

scholarly journals Russellosaurus coheni n. gen., n. sp., a 92 million-year-old mosasaur from Texas (USA), and the definition of the parafamily Russellosaurina

2005 ◽  
Vol 84 (3) ◽  
pp. 321-333 ◽  
Author(s):  
M.J. Polcyn ◽  
G.L. Bell
Keyword(s):  
Phylogenetic Analysis ◽  
North America ◽  
Common Ancestor ◽  
Dallas County ◽  
Close Relationship ◽  
Definition Of ◽  
Basal Position ◽  
Marine Adaptations

AbstractA new mosasaur, Russellosaurus coheni, is described from the Collignoniceras woollgari Zone (lower Middle Turonian) at Cedar Hill, Dallas County, Texas. At approximately 92 Ma, it is the oldest well-preserved mosasaur skull from North America. It possesses characters diagnostic of Plioplatecarpinae but retains numerous plesiomorphies as well. Phylogenetic analysis indicates a close relationship with Yaguarasaurus columbianus, and these two, together with Tethysaurus nopcsai, form a clade that occupies a position basal to the divergence of the subfamilies Tylosaurinae and Plioplatecarpinae. Russellosaurus coheni is proposed as the nominal taxon of a new mosasaur clade, parafamily taxon novum Russellosaurina, which includes Plioplatecarpinae, Tylosaurinae, their common ancestor and all descendants. Tethysaurus retains a plesiopedal limb and girdle morphology, and along with Russellosaurus and Yaguarasaurus, cranial plesiomorphies. Dallasaurus turneri, a temporally and geographically sympatric plesiopedal mosasaur, occupies a basal position within Mosasaurinae. This phyletic arrangement confirms that marine adaptations, such as development of paddle-like limbs, occurred independently in at least two lineages of mosasaurs, once within Mosasaurinae and once within Russellosaurina.

scholarly journals Exploring the relationship of Homalosilpha and Mimosilpha (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10618
Author(s):  
Shuran Liao ◽  
Yishu Wang ◽  
Duting Jin ◽  
Rong Chen ◽  
Zongqing Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Close Relationship ◽  
Relationship Of ◽  
The Relationship ◽  
Six Genes

This study utilized six genes (12S, 16S, 18S, 28S, COII and H3) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera Homalosilpha Stål, 1874 and Mimosilpha Bey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i.e., Homalosilpha obtusangula sp. nov., Homalosilpha recta sp. nov., Homalosilpha alba sp. nov. and Homalosilpha clavellata sp. nov. based on morphological and COI data. A key to the worldwide Homalosilpha is provided.

scholarly journals The tetrapod fauna of the upper Permian Naobaogou Formation of China: 5. Caodeyao liuyufengi gen. et sp. nov., a new peculiar therocephalian

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9160
Author(s):  
Jun Liu ◽  
Fernando Abdala
Keyword(s):  
Phylogenetic Analysis ◽  
Zygomatic Arch ◽  
Upper Permian ◽  
New Taxon ◽  
Late Permian ◽  
Vertebrate Fauna ◽  
Terrestrial Vertebrate ◽  
Close Relationship ◽  
Cladistic Analyses ◽  
Relationship Of

The upper Permian Naobaogou Formation has been the goal of recent contributions that notably increased the knowledge of its terrestrial vertebrate fauna and unravelled a hidden late Permian therocephalian diversity in China. Two very different species of therocephalians have been documented in the Naobaogou Formation and they were recovered as basal akidnognathids in cladistic analyses. In this contribution we describe Caodeyao liuyufengi gen. et sp. nov., represented by a partial skull and mandible, and a humerus. The new taxon features a short, high snout and a wide temporal opening with the coronoid process of the mandible separated by a wide space medially to the zygomatic arch. The latter feature is only recognized in the Russian therocephalian Purlovia maxima and it is also characteristic of non-mammaliaform cynodonts. Phylogenetic analysis indicates a close relationship of the new Chinese taxon with Purlovia maxima, producing a monophyletic Laurasian group in therocephalian phylogeny. With the representation of three different species, the Naobaogou Formation is now the most prolific unit documenting therocephalian late Permian diversity in China.

Validation of Rhabditolaimus Fuchs, 1914 (Nematoda: Diplogastridae) supported by integrative taxonomic evidence

Nematology ◽  
2012 ◽  
Vol 14 (5) ◽  
pp. 595-604 ◽  
Author(s):  
Vladislav Susoy ◽  
Matthias Herrmann
Keyword(s):  
Phylogenetic Analysis ◽  
Central Europe ◽  
Type Species ◽  
Morphological Characters ◽  
Molecular Phylogenetic Analysis ◽  
New Combinations ◽  
Hylobius Abietis ◽  
Type Host ◽  
Close Relationship ◽  
Molecular Phylogenetic

Rhabditolaimus leuckarti, type species of Rhabditolaimus, was isolated from its type host, Hylobius abietis (Coleoptera: Curculionidae), at several locations in central Europe. The position of the species among other diplogastrid nematodes was revised using morphological characters and molecular phylogenetic analysis. The revealed common apomorphic features and the inferred evolutionary tree strongly indicates a close relationship between R. leuckarti and Myctolaimus. Our findings suggest that the historical classifications do not reflect the natural relationships of some diplogastrid taxa. Therefore, we reject all previous synonymisations of Rhabditolaimus and consider it to be valid within the Diplogastridae. Five species are transferred from Diplogasteroides to Rhabditolaimus. Myctolaimus sensu lato is regarded as a junior synonym of Rhabditolaimus and the following new combinations are proposed: R. anoplophorae comb. n., R. carolinensis comb. n., R. curzii comb. n., R. dendrophilus comb. n., R. erectus comb. n., R. goodeyi comb. n., R. inevectus, comb. n., R. kishtwarensis comb. n., R. macrolaimus comb. n., R. nacogdochensis comb. n., R. neolongistoma comb. n., R. pellucidus comb. n., R. platypi comb. n., R. rifflei comb. n., R. robiniae comb. n., R. ulmi comb. n., R. vitautasi comb. n., R. walkeri comb. n. and R. zamithi comb. n.

scholarly journals Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates

2020 ◽  
Vol 12 (7) ◽  
pp. 1060-1073 ◽  
Author(s):  
Dan Shen ◽  
Bo Gao ◽  
Csaba Miskey ◽  
Cai Chen ◽  
Yatong Sang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Horizontal Transfer ◽  
Phylogenetic Analyses ◽  
Land Plant ◽  
Activity Assay ◽  
Animal Kingdom ◽  
Close Relationship ◽  
Recombination Activating Gene ◽  
Multiple Invasions ◽  
Relationship Of

Abstract Although the DD41D (named as Visitor, VS) family of Tc1/mariner transposons was discovered in Arthropods and Mollusca, the evolution profile of this family is still largely unknown. We found that VS is widespread in the animal kingdom, including 140 species of 18 orders in invertebrates and 30 species of 12 orders in vertebrates, and one land plant species. Our data revealed multiple horizontal transfer events in both invertebrates and vertebrates and invasion into multiple lineages of mammals, including Chiroptera (seven species), Dasyuromorphia/Marsupialia (one species), Didelphimorphia/Marsupialia (one species), Diprotodontia/Marsupialia (two species), and Primates (one species). Phylogenetic analysis revealed a close relationship of VSs to DD37D/maT and DD34D/mariner and confirmed that VSs with the DD40D signature identified previously are not a distinct family but originated from DD41D/VS. Age analysis revealed that the most recent invasion of VSs was found in ray-finned fishes and a toad, followed by relatively young invasions in bats and marsupials, whereas VSs in mammals, jawless fishes, and lizards were mainly represented by ancient copies, suggesting old age. Phylogenetic analyses and comparison of pairwise distances between VSs and recombination-activating gene 1 (RAG1) support horizontal transfer events of VSs in vertebrates. The intact VSs from bats were nonfunctional as determined by the transposition activity assay. Some vertebrate lineages and species were identified as the hot hosts of Tc1/mariner transposons. Overall, our study presents the evolution profile of VSs and suggests that VSs play roles in diversifying and shaping the genomes of diverse animal lineages.

scholarly journals Complete Chloroplast Genome Sequences of Three Aroideae Species (Araceae): Lights into Selective Pressure, Marker Development and Phylogenetic Relationships

2021 ◽  
Author(s):  
Bicong Li ◽  
Tao Liu ◽  
Asjad Ali ◽  
Yao Xiao ◽  
Nan Shan ◽  
...  
Keyword(s):  
Dna Barcodes ◽  
Protein Coding ◽  
Variable Regions ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genomes ◽  
Xanthosoma Sagittifolium ◽  
Close Relationship ◽  
Relationship Of ◽  
First Time

Abstract Background : Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are taxonomically perplexing due to shared interspecific morphological traits and variation.Result : This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily.Conclusion : These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

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