Parallelization Mechanisms of Neighbor-Joining for CUDA Enabled Devices

2012 ◽  
Author(s):  
Ran Zheng ◽  
Qiongyao Zhang ◽  
Hai Jin ◽  
Zhiyuan Shao ◽  
Xiaowen Feng
Keyword(s):  
Neighbor Joining

scholarly journals Abundant Mitochondrial Genome Diversity, Population Differentiation and Convergent Evolution in Pines

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1605-1614
Author(s):  
Junyuan Wu ◽  
Konstantin V Krutovskii ◽  
Steven H Strauss
Keyword(s):  
Mitochondrial Dna ◽  
Population Differentiation ◽  
Mitochondrial Gene ◽  
Dna Polymorphisms ◽  
Neighbor Joining ◽  
Closely Related Species ◽  
Breeding Programs ◽  
Length Polymorphisms ◽  
Polymerase Chain ◽  
Mitochondrial Genome Diversity

Abstract We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and θ) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.

scholarly journals Molecular record for the first authentication of Isaria cicadae from Vietnam

2021 ◽  
Vol 16 (1) ◽  
pp. 711-718
Author(s):  
Thuan Duc Lao ◽  
Hanh Van Trinh ◽  
Loi Vuong ◽  
Luyen Tien Vu ◽  
Thuy Ai Huyen Le ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Morphological Analysis ◽  
Phylogenetic Analyses ◽  
Neighbor Joining ◽  
Pcr Assay ◽  
Parsimony Method ◽  
Maximum Parsimony Method ◽  
Cordyceps Cicadae ◽  
High Bootstrap

Abstract The entomopathogenic fungus T011, parasitizing on nymph of Cicada, collected in the coffee garden in Dak Lak Province, Vietnam, was preliminarily morphologically identified as Isaria cicadae, belonged to order Hypocreales and family Clavicipitaceae. To ensure the authenticity of T011, phylogenetic analysis of the concatenated set of multiple genes including ITS, nrLSU, nrSSU, Rpb1, and Tef1 was applied to support the identification. Genomic DNA was isolated from dried sample T011. The PCR assay sequencing was applied to amplify ITS, nrLSU, nrSSU, Rpb1, and Tef1 gene. For phylogenetic analysis, the concatenated data of both target gens were constructed with MEGAX with a 1,000 replicate bootstrap based on the neighbor-joining, maximum likelihood, maximum parsimony method. As the result, the concatenated data containing 62 sequences belonged to order Hypocreales, families Clavicipitaceae, and 2 outgroup sequences belonged to order Hypocreales, genus Verticillium. The phylogenetic analysis results indicated that T011 was accepted at subclade Cordyceps and significantly formed the monophyletic group with referent Cordyceps cicadae (Telemorph of Isaria cicadae) with high bootstrap value. The phylogenetically analyzed result was strongly supported by our morphological analysis described as the Isaria cicadae. In summary, phylogenetic analyses based on the concatenated dataset were successfully applied to strengthen the identification of T011 as Isaria cicadae.

scholarly journals Neighbor-Joining Revealed

2006 ◽  
Vol 23 (11) ◽  
pp. 1997-2000 ◽  
Author(s):  
O. Gascuel
Keyword(s):  
Neighbor Joining

scholarly journals Two new species of Undifilum, fungal endophytes of Astragalus (locoweeds) in the United States

Botany ◽  
2012 ◽  
Vol 90 (9) ◽  
pp. 866-875 ◽  
Author(s):  
Deana L. Baucom ◽  
Marie Romero ◽  
Robert Belfon ◽  
Rebecca Creamer
Keyword(s):  
New Species ◽  
New Mexico ◽  
Random Amplified Polymorphic Dna ◽  
Phylogenetic Analyses ◽  
Fungal Endophytes ◽  
Morphological Characteristics ◽  
Its Region ◽  
The United States ◽  
Neighbor Joining

New species of Undifilum , from locoweeds Astragalus lentiginosus Vitman and Astragalus mollissimus Torr., are described using morphological characteristics and molecular phylogenetic analyses as Undifilum fulvum Baucom & Creamer sp. nov. and Undifilum cinereum Baucom & Creamer sp. nov. Fungi were isolated from dried plants of A. lentiginosus var. araneosus , diphysus , lentiginosus , and wahweapensis collected from Arizona, Oregon, and Utah, USA, and A. mollissimus var. biglovii , earleii , and mollissimus collected from New Mexico, Oklahoma, and Texas, USA. Endophytic fungi from Astragalus locoweeds were compared to Undifilum oxytropis isolates obtained from dried plant material of Oxytropis lamberteii from New Mexico and Oxytropis sericea from Arizona, Colorado, New Mexico, Utah, and Wyoming. Extremely slow growth in vitro was observed for all, and conidia, if present, were ellipsoid with transverse septa. However, in vitro color, growth on four different media, and conidium size differed between fungi from Astragalus spp. and U. oxytropis. Neighbor-joining analyses of internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GPD) gene sequences revealed that U. fulvum and U. cinereum formed a clade distinct from U. oxytropis. This was supported by neighbor-joining analyses of results generated from random amplified polymorphic DNA (RAPD) fragments using two different primers.

scholarly journals Random Amplification of Polymorphic DNA Analysis for Genetic Characterization of Two Breeds of Dogs, German Shepherd and Japanese Spitz

2013 ◽  
Vol 13 (2) ◽  
pp. 73-78
Author(s):  
Jarina Joshsi ◽  
Lumanti Manandhar ◽  
Patima Shrestha ◽  
Rani Gupta ◽  
Rojlina Manadhar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Neighbor Joining ◽  
German Shepherd ◽  
Polymorphic Loci ◽  
Random Amplification

Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity in dog samples belonging to populations of German Shepherd and Japanese Spitz. A total of twelve samples were typed using eight RAPD primers. Out of eight primers, three primers gave result in six individuals of dogs. The phylogenetic tree constructed by the neighbor joining method based on Nei. Original measures revealed highest genetic identity found in German Shepherd as 0.9444 and highest genetic distance as 1.2809. The analysis predicts the number of polymorphic loci as 15 and the percentage of polymorphic loci as 83.3. Nepal Journal of Science and Technology Vol. 13, No. 2 (2012) 73-78 DOI: http://dx.doi.org/10.3126/njst.v13i2.7717

Phyllocnistis podocarpa sp. nov. (Lepidoptera, Gracillariidae), a buddhist pine leaf-miner from Japan: taxonomy, DNA barcodes, damage and parasitoids

Zootaxa ◽  
2018 ◽  
Vol 4422 (4) ◽  
pp. 558 ◽  
Author(s):  
TENGTENG LIU ◽  
JIE SUN ◽  
BO CAI ◽  
YING WU
Keyword(s):  
Economic Value ◽  
Iucn Red List ◽  
Red List ◽  
Leaf Miner ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Parasitoid Species ◽  
Frontal Process ◽  
Podocarpus Macrophyllus ◽  
Garden Plant

Phyllocnistis podocarpa sp. nov., is described from mines in Podocarpus macrophyllus (Family Podocarpaceae). The host plant P. macrophyllus, also known as buddhist pine on the IUCN Red List, is a noticeable garden plant and thus of high economic value. Buddhist pine has been introduced to many other countries from its native habitat in southern Japan. Special attention has been paid for it during the overseas import in China. The morphology of the pupae of P. podocarpa, particularly the frontal process of the head and the spine clusters on terga, ones of the most useful diagnostic characters for species identification of Phyllocnistis on morphology, is demonstrated using SEM. Two parasitoid species of Eulophidae (Hymenoptera) are identified and illustrated. COI barcode sequences are provided along with a Neighbor Joining Tree covering related species for aiding identification. 

scholarly journals Phylogenetic analysis of spring viremia of carp virus (SVCV) identified in Poland

2019 ◽  
Vol 75 (01) ◽  
pp. 6159-2019
Author(s):  
JOANNA MAJ-PALUCH ◽  
EWA BORZYM ◽  
MAREK MATRAS ◽  
MAGDALENA STACHNIK ◽  
MICHAŁ REICHERT
Keyword(s):  
Phylogenetic Analysis ◽  
Preventive Measures ◽  
Genetic Material ◽  
Point Mutations ◽  
The United States ◽  
Nucleotide Sequence Analysis ◽  
Neighbor Joining ◽  
The Czech Republic ◽  
Virus Isolates ◽  
Family Rhabdoviridae

Spring viremia of carp (SVC) is a disease caused by a virus belonging to the genus Vesiculovirus, family Rhabdoviridae. The SVC virus is divided into four genogroups, Ia, Ib, Ic, and Id, due to its geographical distribution. This study aimed to identify the genotype of the SVC virus circulating in Poland. Polish SVC virus isolates were propagated on EPC and FHM cell lines, and genetic material (RNA) was isolated. The virus was detected in test samples by reverse transcription, sequenced and analyzed using MEGA 6.06 software. The phylogenetic tree was constructed by the Neighbor-Joining method. The results of phylogenetic analysis revealed the presence of two genogroups of the SVC virus in Poland. Most of Polish isolates belonged to the genogroup Id, as do isolates AY196200 from the Czech Republic, Z37505 from Belgium and EF593149 from the United States. Only two Polish isolates from Silesian Voivodeship were more closely related to Chinese and US isolates belonging to the genogroup Ia. There were no isolates belonging to the genogroups Ib and Ic. Nucleotide sequence analysis revealed certain point mutations between particular isolates. Knowledge on the genetic variants of the SVC virus circulating in Poland will be useful in epizootic investigations and preventive measures to protect Polish aquaculture from new variants from the neighboring countries

scholarly journals Phylogenetic relationships among different morphotypes of StY-genomic species Elymus ciliaris and E. amurensis (Poaceae) as a unified macroevolutional complex

2021 ◽  
Author(s):  
Alexander V. Agafonov ◽  
◽  
Elena V. Shabanova ◽  
Maria V. Emtseva ◽  
Sergei V. Asbaganov ◽  
...  
Keyword(s):  
Early Treatment ◽  
Morphological Traits ◽  
Nuclear Gene ◽  
Experimental Methods ◽  
Component Composition ◽  
Issr Markers ◽  
Neighbor Joining ◽  
Genomic Species ◽  
Protein Spectra ◽  
Far Eastern

Microevolutionary relationships between the Far Eastern StY-genomic species Elymus ciliaris and E. amurensis were studied using a set of experimental methods. No relationship was found between the formal species affiliation of a particular accession and the component composition of protein spectra. The consensus neighbor-joining (NJ) dendrogram based on the variability of ISSR markers showed the features of differentiation among different morphotypes of the two species. Pubescence of leaf blades is not a marker of differences between the studied species. A level of crossability in E. ciliaris s. l. did not allow to study the inheritance of morphological traits. According to the results of sequencing of the nuclear gene GBSS1, the sequences of the St subgenome are the most informative in terms of microevolutionary differentiation. It is proposed to return to the early treatment by N.N. Tsvelev, where E. ciliaris and E. amurensis were considered as subspecies of E. ciliaris s. l.

scholarly journals A new species of Pima Hulst, 1888 from China (Lepidoptera, Pyralidae, Phycitinae), with a key to Holarctic species

ZooKeys ◽  
2020 ◽  
Vol 975 ◽  
pp. 111-124
Author(s):  
Linlin Yang ◽  
Yingdang Ren
Keyword(s):  
New Species ◽  
Species Delimitation ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Distribution Map ◽  
Autonomous Region ◽  
Ningxia Hui Autonomous Region ◽  
Lepidoptera Pyralidae ◽  
A New Species ◽  
Holarctic Species

Pima tristriatasp. nov. is described as new to science based on specimens collected from the Ningxia Hui Autonomous Region, China, and P. boisduvaliella (Guenée, 1845) is also treated here for comparison. DNA barcodes of the two species are provided, together with a neighbor-joining tree for species delimitation. A key to the Holarctic species and a distribution map of the Chinese species are presented.

scholarly journals Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2025
Author(s):  
Shyryn Almerekova ◽  
Yuliya Genievskaya ◽  
Saule Abugalieva ◽  
Kazuhiro Sato ◽  
Yerlan Turuspekov
Keyword(s):  
Population Structure ◽  
Heading Date ◽  
Snp Markers ◽  
Principal Coordinate Analysis ◽  
Neighbor Joining ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Ancestral Node

The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.

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