scholarly journals Molecular phylogeny and species delimitation of the genus Tonkinacris (Orthoptera, Acrididae, Melanoplinae) from China

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249431
Author(s):  
Haojie Wang ◽  
Bing Jiang ◽  
Jingxiao Gu ◽  
Tao Wei ◽  
Liliang Lin ◽  
...  
Keyword(s):  
Nuclear Ribosomal Dna ◽  
Species Boundaries ◽  
Molecular Evidence ◽  
Phylogenetic Species Concept ◽  
Interspecific Divergence ◽  
Parsimony Network ◽  
Statistical Parsimony ◽  
Complete Sequences ◽  
Nj Tree ◽  
Independent Species

Tonkinacris is a small group in Acrididae. While a few species were occasionally sampled in some previous molecular studies, there is no revisionary research devoted to the genus. In this study, we explored the phylogeny of and the relationships among Chinese species of the genus Tonkinacris using the mitochondrial COI barcode and the complete sequences of ITS1 and ITS2 of the nuclear ribosomal DNA. The phylogeny was reconstructed in maximum likelihood and Bayesian inference frameworks, respectively. The overlap range between intraspecific variation and interspecific divergence was assessed via K2P distances. Species boundaries were delimitated using phylogenetic species concept, NJ tree, K2P distance, the statistical parsimony network as well as the GMYC model. The results demonstrate that the Chinese Tonkinacris species is a monophyletic group and the phylogenetic relationship among them is (T. sinensis, (T. meridionalis, (T. decoratus, T. damingshanus))). While T. sinensis, T. meridionalis and T. decoratus were confirmed being good independent species strongly supported by both morphological and molecular evidences, the validity of T. damingshanus was not perfectly supported by molecular evidence in this study.

ITS sequence variation supports the hybrid origin of Malus toringoides Hughes

2007 ◽  
Vol 85 (7) ◽  
pp. 659-666 ◽  
Author(s):  
Ting-Ting Feng ◽  
Zhi-Qin Zhou ◽  
Jian-Min Tang ◽  
Ming-Hao Cheng ◽  
Shi-Liang Zhou
Keyword(s):  
Sequence Variation ◽  
Gene Tree ◽  
Natural Populations ◽  
Its Sequences ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Putative Hybrid ◽  
Molecular Evidence ◽  
Sequence Information ◽  
Aflp Data

Malus toringoides (Rehd.) Hughes was suggested to have originated from hybridization between Malus transitoria Schneid. and Malus kansuensis Rehd., followed by repeated backcrossing to one of the putative parents. In the present study, the sequence information of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA) was used to re-examine the origin of this species. A total of 69 accessions from three natural populations (Maerkang, Xiaba and Kehe, Aba Autonomous Region, Sichuan, China) of M. toringoides and 10 accessions of its putative parents were analyzed. Using Malus angustifolia (Ait.) Michx., Malus ioensis (Wood) Britt. and Malus doumeri Chev. as outgroups, our phylogenetic analysis of the ITS sequences of M. toringoides and its putative parents showed that M. toringoides was not monophyletic, and two different types of ITS sequences which were obtained from each of the six accessions of M. toringoides were found to have clustered separately with those of the two putative parent species on the gene tree. A comparison of the sequence variation between M. toringoides and its putative parents revealed an additive variation pattern of ITS sequences in the putative hybrid species. These results are consistent with the previous morphological and amplified fragment length polymorphism (AFLP) data which suggested that M. toringoides was of hybrid origin. Our ITS data provide new molecular evidence for the hybrid origin hypothesis of M. toringoides and these results are of great importance for future study on hybridization, polyploid speciation and evolution of the genus Malus Miller.

Towards a new classification of tribe Stachydeae (Lamiaceae): naming clades using molecular evidence

2019 ◽  
Vol 190 (4) ◽  
pp. 345-358 ◽  
Author(s):  
Yasaman Salmaki ◽  
Günther Heubl ◽  
Maximilian Weigend
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
New Classification ◽  
Formal Classification ◽  
Phylogenetic Nomenclature

AbstractStachydeae, comprising c. 470 species, are one of the most diverse and taxonomically puzzling groups in Lamioideae. In the present study, the phylogenetic relationships in the Eurystachys clade (a phylogenetic name for all genera attributed to Stachydeae except Melittis) were reconstructed utilizing nuclear ribosomal DNA sequences (nrETS, 5S-NTS) from 148 accessions in 12 genera. Our phylogenetic results recovered Stachys as paraphyletic with numerous traditionally recognized genera nested in it. A broadly defined Eurystachys clade, however, was monophyletic. Unlike previous studies, the present study was able to resolve the group into 12 well-supported clades, named here as (1) Eriostomum, (2) Stachys, (3) Prasium, (4) Setifolia, (5) Distantes, (6) Burgsdorfia, (7) Hesiodia, (8) Empedoclia, (9) Sideritis, (10) Marrubiastrum, (11) Swainsoniana and (12) Olisia. These 12 clades were formally named in a phylogenetic nomenclature for the Eurystachys clade. Several infrageneric units were retrieved as monophyletic, namely Sideritis sections Burgsdorfia, Empedoclia and Hesiodia, Sideritis subgenus Marrubiastrum and Stachys sections Eriostomum (including Stachys section Mucronata) and Setifolia. The findings of this study also provide the basis for a future formal classification, with two options: (1) splitting of the Eurystachys clade into 12 monophyletic genera, all of them based on pre-existing genus names and redefined to encompass additional taxa, but without clear morphological apomorphies; or (2) lumping of all segregates into a broadly defined Stachys, including widely recognized and well-defined segregates such as Prasium and Sideritis.

Reinstatement and lectotypification of Bridelia fordii (Phyllanthaceae)

Phytotaxa ◽  
2015 ◽  
Vol 226 (3) ◽  
pp. 295 ◽  
Author(s):  
Yongquan Li ◽  
Gang Yao
Keyword(s):  
Molecular Evidence ◽  
Independent Species

Bridelia fordii, originally described from China in 1894, often treated as a synonym of B. retusa. Upon examinating the types and other related specimens, we conclude that the former is easily distinguishable from the latter and the former should be accepted as an independent species. Our previous molecular evidence also supports this conclusion. We further designate the lectotype of B. fordii in this study.

Origin and evolution of the Italian subterranean termite Reticulitermes lucifugus (Blattodea, Termitoidae, Rhinotermitidae)

2013 ◽  
Vol 103 (6) ◽  
pp. 734-741 ◽  
Author(s):  
A. Luchetti ◽  
V. Scicchitano ◽  
B. Mantovani
Keyword(s):  
Gene Marker ◽  
Data Set ◽  
Origin And Evolution ◽  
Anticlockwise Rotation ◽  
Parsimony Network ◽  
Statistical Parsimony ◽  
Coii Gene ◽  
Cytochrome Oxidase Ii ◽  
Diversity Estimates ◽  
Mitochondrial Cytochrome Oxidase

AbstractThe Holarctic genus Reticulitermes shows seven species within the Mediterranean Basin. While phylogeny and systematics at continental level has been deeply investigated, a few studies concentrated on local ranges. To gain a clearer picture of the diversity and evolution of the Italian species Reticulitermes lucifugus, we analyzed the mitochondrial cytochrome oxidase II (COII) gene marker in newly collected colonies across the Peninsula. Data were gathered with all R. lucifugus sequences available from previous studies; COII sequences of the closely related Iberian taxa were also added to the data set. Maximum-likelihood, median-joining and statistical parsimony network elaborations on the resulting 119 colonies all agreed in indicating that: (i) the Sardo-Corsican subspecies R. lucifugus corsicus, strictly related to Southern Italian populations (including the Sicilian ones), is phylogenetically closer to the Iberian Reticulitermes grassei; and (ii) R. lucifugus lucifugus peninsular populations are structured into three clusters. The phylogenetic relationships and the biogeography of extant taxa suggest a scenario in which R. lucifugus ancestors colonized the Italian region through the Sardo-Corsican microplate during its Oligocene-Miocene anticlockwise rotation. Moreover, well after the colonization took place, northward range expansion might have produced the presently observed genetic diversity, as inferred from haplotype and nucleotide diversity estimates. On the whole, this study highlights the evolution of Italian Reticulitermes taxa and supports the importance of a wide taxon sampling especially when dealing with organisms easily dispersed by human activities.

scholarly journals Phylogenetic analysis of the genus Conringia Heist. Ex Fabr. (Brassicaceae) in Turkey based on nuclear (nrITS) and chloroplast (trnL-F) DNA sequences

2021 ◽  
Vol 13 (3) ◽  
pp. 11034
Author(s):  
Emre SEVINDIK ◽  
Melike AYDOGAN ◽  
Mehmet Y. PAKSOY
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nuclear Ribosomal Dna ◽  
Neighbor Joining ◽  
F Region ◽  
Brassicaceae Species ◽  
Nj Tree ◽  
Brassicaceae Family

In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while the trnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic.

Morphological and molecular evidence reveals a new species of Lyperosomum Looss, 1899 (Digenea: Dicrocoeliidae) from Melanerpes aurifrons (Wagler, 1829) from northern Mexico

2020 ◽  
Vol 94 ◽  
Author(s):  
M.T. González-García ◽  
M.P. Ortega-Olivares ◽  
L. Andrade-Gómez ◽  
M. García-Varela
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Nuclear Ribosomal Dna ◽  
Bootstrap Support ◽  
Molecular Evidence ◽  
Congeneric Species ◽  
Northern Mexico ◽  
A New Species ◽  
Cox 1

Abstract A new species of the genus Lyperosomum Looss, 1899, from the intestine of the golden-fronted woodpecker (Melanerpes aurifrons) from northern Mexico is described. Lyperosomum cuauhxinqui sp. n. is morphologically distinguished from other congeneric species from the Americas by a higher oral/ventral sucker ratio and its body length and width. The sequences of domains D1–D3 of the large subunit (LSU) of nuclear ribosomal DNA and cytochrome c oxidase subunit 1 (cox 1) from the mitochondrial DNA of the new species were obtained and compared with available sequences from GenBank. The genetic divergence estimated between the new species and other congeneric species ranged from 2 to 6% and 13.4 to 17.3% for LSU and cox 1, respectively. Phylogenetic analyses based on the two (LSU and cox 1) molecular markers consistently showed that L. cuauhxinqui sp. n. was nested within the genus Lyperosomum, with strong bootstrap support (100%) and Bayesian posterior probabilities (1.0). In particular, the LSU tree indicated that the sequence of the new species is closely related to sequences from Zonorchis alveyi, Zonorchis delectans and Zonorchis sp. from Central America, suggesting that these sequences should be transferred to the genus Lyperosomum. The new species represents the first record from Mexico and the fifth species identified in the Americas. Our study also revealed that the taxonomy of the genus Lyperosomum should be re-examined by combining molecular, morphological and ecological characteristics.

Allium dönmezii, a new species of Allium sect. Melanocrommyum (Amaryllidaceae) from Turkey: morphological and molecular evidence

Phytotaxa ◽  
2019 ◽  
Vol 411 (3) ◽  
pp. 194-204
Author(s):  
ŞÜKRÜ KARAKUŞ ◽  
BİROL MUTLU
Keyword(s):  
New Species ◽  
Molecular Marker ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
Its Regions ◽  
First Time ◽  
East Anatolia ◽  
A New Species

Allium dönmezii is described as a new species from east Anatolia, Turkey. The molecular marker ITS (Internal Transcribed Spacer of nuclear ribosomal DNA) confirms that the new species belongs to A. sect. Melanocrommyum. The diagnostic characters of the new species are morphologically compared with the related A. woronowii, A. serpentinicum, and A. moderense, as well as with A. rothii and A. chrysantherum. In addition, the ITS regions of A. purpureoviride and A. chrysantherum were sequenced and uploaded on GenBank for the first time.

Xanthagaricus siamensis sp. nov. (Agaricaceae), a new species with dull green lamellae from northern Thailand

Phytotaxa ◽  
2020 ◽  
Vol 437 (1) ◽  
pp. 14-22
Author(s):  
YUAN S. LIU ◽  
JIAN-KUI (JACK) LIU ◽  
PHONGEUN SYSOUPHANTHONG ◽  
KEVIN D. HYDE ◽  
SAISAMORN LUMYONG
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
Internal Transcribed Spacer Region ◽  
Northern Thailand ◽  
A New Species

Xanthagaricus siamensis, a new species in the family Agaricaceae, was discovered in northern Thailand and is here introduced based on its morphological features and molecular data. It is characterized by small to medium-sized basidiomata, a convex to plano-convex with depressed center pileus when mature, the presence of greyish orange to violet-brown fibrillose squamules on the pileus, lamellae that start out white, change to pinkish white when damaged, then change to dull green with age. Additionally, the annulus is fugacious, and the pileipellis is recognized as a cutis which morphologically distinguishes it from all other known Xanthagaricus. Phylogenetic analysis of the internal transcribed spacer region (ITS) and the large subunit of the nuclear ribosomal DNA (nrLSU) sequence data indicated that the three specimens of X. siamensis form a distinct lineage within Xanthagaricus, and they formed a well-supported clade representing the genus Xanthagaricus. Detailed illustrations of macro- and micro-morphological characteristics and descriptions are provided, as well as other relevant molecular evidence.

Taxonomic delimitation of endemic Ficus amplocarpa and Ficus dalhousiae Complexes (Moraceae) by DNA barcoding

Phytotaxa ◽  
2020 ◽  
Vol 436 (1) ◽  
pp. 21-35 ◽  
Author(s):  
KARTHIKEYAN MAHIMA ◽  
JANA VENKATA SUDHAKAR ◽  
SATHISHKUMAR RAMALINGAM
Keyword(s):  
Bayesian Analysis ◽  
Dna Barcoding ◽  
Morphological Characters ◽  
Species Boundaries ◽  
Andaman And Nicobar Islands ◽  
Closely Related Species ◽  
North Eastern ◽  
Nicobar Islands ◽  
Nuclear Loci ◽  
Independent Species

Ficus L. species are extensively diversified in India representing North-eastern states, peninsular region and Andaman and Nicobar Islands among which ten species are endemic. Thus closely related species confuses taxonomists and evolutionary researchers. Our study aims to distinguish the highly endangered closely allied species of Ficus genus with persistent variation. The first study complex includes Ficus dalhousiae and Ficus anamalayana and the second complex includes Ficus amplocarpa, Ficus guttata and Ficus laevis. The species in each complex groups are hard to distinguish because of their highly similar morphological characters. To resolve the taxonomical disputes, the nuclear loci ITS2 and chloroplast loci trnH-psbA were used to reconstruct the phylogenetic relationship to understand the species boundaries. In our results, intra-specific divergence is not found in the two markers tested however, the total inter-specific divergence between F. dalhousiae and F. anamalayana is found to be 6.5% and in the case of F. amplocarpa and F. guttata is to be 8.5%. The highest divergence is observed in trnH-psbA (0.991 ± 0.713) followed by ITS2 (0.149 ± 0.064). Bayesian analysis showed a clear segregation between F. amplocarpa and F. guttata suggesting that they could be independent species not a variety of F. laevis. Similarly, bayesian analysis of F. dalhousiae and F. anamalayana results support that they can be treated as different species. Thereby, our study suggests that species within taxonomically complex group can be resolved by DNA barcoding.

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