nj tree
Recently Published Documents


TOTAL DOCUMENTS

53
(FIVE YEARS 30)

H-INDEX

4
(FIVE YEARS 2)

Author(s):  
Kartika Senjarini ◽  
Lailly Nur Uswatul Hasanah ◽  
Miatin Alvin Septianasari ◽  
Muhammad Khalid Abdullah ◽  
Rike Oktarianti ◽  
...  

The presence of intraspecies variations of An. vagus later categorized as the subspecies of An. vagus vagus and An. vagus limosus, could be an obstacle to the identification process, which is an important step for malaria vector’s competence characterization. Based on morphological identification, those subspecies could be distinguished by the presences of pale scales in prehumeral and pale bands  in proboscis. The objective of this research was to compare subspecies complexes of An. vagus morphologically and molecularly using Internal Transcribed Spacer 2 (ITS2). Anopheles samples were collected from Bangsring, Banyuwangi. Their phylogenetic tree was constructed by using NJ method based on their ITS2 sequences. BLAST result showed that An. vagus vagus and An. vagus limosus were similar to An. vagus FJ654649.1 from East Java Indonesia and East Timor based on its 99% homology and their molecular distance. The Neighbour Joining (NJ) tree grouped those subspecies in one clade with a boostrap value of 82%. This subspeciation might be due to the different rates of evolution. ITS2 sequences of An. vagus vagus and An. vagus limosus were submitted to GenBank with the accession number of MW314227.1 and MW319822.1, respectively. Kemunculan variasi intraspesies An. vagus yang kemudian dikategorikan sebagai subspesies An. vagus vagus dan An. vagus limosus menjadi kendala dalam proses identifikasi yang merupakan langkah penting dalam menentukan kompetensi vektor malaria. Berdasarkan karakter morfologi, subspesies tersebut dibedakan dengan adanya sisik pucat pada bagian prehumeral dan pita pucat pada probosis. Penelitian ini bertujuan untuk membandingkan subspesies An. vagus secara morfologis dan molekuler menggunakan Internal Transcribed Spacer 2 (ITS2). Nyamuk Anopheles didapatkan dari Bangsring, Banyuwangi. Konstruksi pohon filogeni dilakukan berdasarkan sekuen ITS2 yang dianalisis menggunakan metode NJ. Hasil BLAST menunjukkan, ITS2 An. vagus vagus dan An. vagus limosus memiliki tingkat homologi 99% dan jarak evolusi molekuler terendah dengan An. vagus FJ654649.1 dari Jawa Timur Indonesia dan Timor Timur. Pohon NJ mengelompokkan subspesies tersebut dalam satu klade dengan nilai boostrap 82%. Hal ini dapat terjadi karena perbedaan kecepatan evolusi yang memungkinkan terjadinya subspesiasi. Urutan basa ITS2 dari An. vagus vagus dan An. vagus limosus telah didaftarkan ke GenBank dengan nomor aksesi MW314227.1 dan MW319822.1.


Author(s):  
BOYANG AN ◽  
DANYANG YIN ◽  
SONGLIN HUANG ◽  
TARIQ AHMAD ◽  
Li Bo

The classification of some Turdus species, such as the Naumann’s and dusky thrush complexes and the red-throated and black-throated thrush complexes, is controversial. Herein, we used molecular data (mitochondrial genes and microsatellite loci) and morphological characters to review the taxonomy of these thrush complexes and analyze the genetic differentiation between them. Our phylogenetic analysis based on mitochondrial genes indicated that all haplotypes could be divided into two reciprocally monophyletic sister clades corresponding to these two thrush complexes. The same results were revealed by coalescence-based species delimitation. Therefore, these two thrush complexes should be divided into two separate species (T. naumanni and T. ruficollis) and include two subspecies per species according to combined characters from morphological analyses and multilocus approaches. The above classifications were also supported by an analysis of genetic differentiation between T. naumanni and T. ruficollis and within each species. Moreover, there was significant mixing between these two thrush species in the neighbor-joining (NJ) tree and the cluster analysis of microsatellite loci. This led to a pattern of nuclear-mitochondrial discordance between the two species. This could be the result of extensive nuclear introgression between these two sister species. We also provide a potential explanation for the mechanism of gene introgression and nuclear-mitochondrial discordance between the two bird species.


Author(s):  
Ciar O’Toole ◽  
Karl P. Phillips ◽  
Caroline Bradley ◽  
Jamie Coughlan ◽  
Eileen Dillane ◽  
...  

Although historical records of introductions that trigger successful biological invasions are common, subsequent patterns of dispersal and colonisation routes are unclear. We use microsatellites to examine genetic population structuring of established invasive brown trout (Salmo trutta) populations in Newfoundland, Canada, for evidence of “natural” dispersal, human-mediated introductions, and colonisation routes. We also explored ancestry of contemporary populations relative to presumed progenitors. Results analysed using STRUCTURE, DAPC, a NJ tree and FST comparisons support records of historical introductions; current Newfoundland populations are largely descended from Scottish stock, with St. John’s the primary introduction site. Subsequent dispersal of these trout was facilitated principally by anadromy, largely consistent with a classic stepping-stone model, with significant isolation-by-distance. With one exception, dispersal along the north and south coasts of the Avalon peninsula appears to be natural and independent, involving stochastic processes resulting in unique outcomes for population composition. This study is a good example of dispersal patterns during a contemporary invasion underscoring the potential for non-anadromous founders to re-express anadromy, facilitating colonization of distant sites.


2021 ◽  
Author(s):  
Zhisen Luo ◽  
Murong Yi ◽  
Kangwen Qiu ◽  
Sibiao Liu ◽  
Sui Gu ◽  
...  

Abstract In this study, two new records of goatfishes Upeneus spottocaudalis and U. sundaicus from the South China Sea, combing evidence from morphology and DNA barcodes for species identification. ML tree and NJ tree result showed that the sequences of U. spottocaudalis and U. sundaicus were clustered with the homologous sequences form GenBank, respectively, and the intraspecific genetic distances of U. spottocaudalis (0.2%) and U. sundaicus (0.3%) were less than 2%. Automatic Barcode Gap Discovery (ABGD) analysis also supported this result of classification.


2021 ◽  
Author(s):  
Arjun Ramachandran ◽  
A. V. Santhoshkumar ◽  
Deepu Mathew ◽  
Manju Elizabeth ◽  
Jiji Joseph ◽  
...  

Abstract Pyrenacantha volubilis Wight. is a dioecious liana occurring in small, clustered populations. The species had no documented use until the recent past, when it was identified to be a source of a highly traded anti-cancer drug – camptothecin. In the present study, we examine the genetic diversity of 12 fragmented natural populations of P. volubilis using morphological and molecular traits. Twelve polymorphic Inter Simple Sequence Repeat (ISSR) primers and 29 agromorphological traits were used to discriminate the populations using UPGMA and NJ tree algorithms respectively. The ISSR amplicon profile had 133 distinct bands. The maximum number of amplicons were produced by UBC 844 (20 bands) and the average polymorphism was 80.07 per cent. The dendrograms obtained based on molecular and agro-morphological data are in close congruence. The Thiruvananthapuram population stood apart in both the analyses as a discrete outgroup: perhaps a consequence of local adaptation. Substantial genetic diversity exists among populations. This could be tapped in domestication, which is the only way forward for the long-term survival of this species. We also report for the first time a standardized method for extraction of genomic DNA from the leaves of P. volubilis.


2021 ◽  
Vol 13 (3) ◽  
pp. 11034
Author(s):  
Emre SEVINDIK ◽  
Melike AYDOGAN ◽  
Mehmet Y. PAKSOY

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.


2021 ◽  
Author(s):  
Yunyun Gao ◽  
Yajun Fu ◽  
Liping Yan ◽  
Defu Hu ◽  
Benmo Jiang ◽  
...  

Abstract BackgroundMyiasis is an infestation of maggots on living tissue in humans and animals all over the world. It is known to occur in wild animals, while no information is reported in forest musk deer. We found a case of traumatic myiasis of an injured forest musk deer (Moschus berezovskii), the wound of which was infected by numerous maggots, and the fur was covered by clusters of eggs. The affected individual was clinically treated immediately and recovered. MethodsDNA barcoding is an efficient technique for species diagnosis, therefore is employed to identify the blowfly samples collected from the infected forest musk deer. Firstly, we extracted genomic DNA from larvae and eggs respectively. The DNA barcoding sequences of 49 individuals were obtained and subsequently analyzed calculating nucleotide composition and divergence and haplotypes, constructing a neighbor-joining (NJ) tree, for accurate identification of these blowflies. ResultsOur results suggest that the average nucleotide divergence between the 49 sequences of blowfly samples is 0.0022, 0.0054 is between sequences of blowfly samples and Lucilia caesar (Linnaeus, 1758) (Diptera: Calliphoridae). Furthermore, the NJ tree construction indicates that the flies collected from the forest musk deer are clustered together with L. caesar. The sequences of sampled blowflies have nine haplotypes, including two shared haplotypes, with haplotype diversity 0.588, nucleotide diversity 0.00215, and the average number of nucleotide differences was 1.374. ConclusionsWe report traumatic myiasis of forest musk deer for the first time, which expands the information on parasite and myiasis of forest musk deer and confirmed the potential risk of traumatic myiasis of forest musk deer.


Zootaxa ◽  
2021 ◽  
Vol 4975 (2) ◽  
pp. 253-272
Author(s):  
MEILING ZHENG ◽  
HOUHUN LI

The Chinese fauna of Psoricoptera Stainton, 1854 included two described species prior to this study. In the present paper we describe three new species: P. curva sp. nov., P. minutignatha sp. nov. and P. proximikawabei sp. nov. P. speciosella Teich, 1893 is recorded from China for the first time. The total number of Psoricoptera species in China is brought to six. The female of P. latignathosa is described for the first time. Photographs of adults and genitalia are provided, along with a key to the Chinese species. A Neighbor-Joining (NJ) tree is provided for species identification and association of the sexes.  


PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249431
Author(s):  
Haojie Wang ◽  
Bing Jiang ◽  
Jingxiao Gu ◽  
Tao Wei ◽  
Liliang Lin ◽  
...  

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.


2021 ◽  
Vol 14 ◽  
pp. 194008292110173
Author(s):  
Xuena Xie ◽  
Haoting Ye ◽  
Xuan Cai ◽  
Chan Li ◽  
Fang Li ◽  
...  

Background Smuggling and illegal trade of pangolins and their scales has drastically reduced the wild population of pangolins. Accurate species identification is currently in urgent need as a powerful weapon for combating pangolin smuggling and trade and conserving the already endangered pangolin species. Aim of the study To develop an efficient method based on DNA mini-barcodes for accurate pangolin species identification and authentication of processed pangolin scales against the non-target species. Materials and methods The primers for amplifying the DNA mini-barcodes were designed based on cytochrome C oxidase subunit I (COI) gene fragments. The mini-barcodes were compared with the two universal barcodes (COI and Cytb) for performance in pangolin species identification by calculating the Kimura-2-parameter (K2P) distance, assessing the clustering dendrogram, and analyzing the BLAST similarity and barcoding gap. The accuracy of the three barcodes was also compared for authentication of pangolin scales against non-target species. Results Comparison of the three barcodes showed that the mini-barcode form COI had the highest amplification success rate (100%) and high variable sites (40.0%), with the ratio of mean inter- to intraspecific distance ratio was 25 and a distinct DNA barcoding gap. In the neighbor-joining (NJ) tree constructed based on the mini-barcode regions, each species of the pangolin family formed an obvious clade respectively, and the clades were all separated from those of the non-target species, indicating that the genetic information in the mini-barcode was sufficient for species identification. Conclusion The DNA mini-barcodes based on COI gene fragments provide an effective and accurate method for identification of pangolin species and authentication of pangolin scale products.


Sign in / Sign up

Export Citation Format

Share Document