Fast algorithm for constructing neighbor-joining phylogenetic trees

To improve the performance of Saitou and Nei＇s algorithm （SN） and Studier and Keppler＇s improved algorithm （SK） for constructing neighbor-joining phylogenetic trees and reduce the time complexity of the computation, a fast algorithm is proposed. The proposed algorithm includes three techniques. First, a linear array A[N] is introduced to store the sum of every row of the distance matrix （the same as SK）, which can eliminate many repeated computations. Secondly, the value of A [i] is computed only once at the beginning of the algorithm, and is updated by three elements in the iteration. Thirdly, a very compact formula for the sum of all the branch lengths of operational taxonomic units （OTUs） i and j is designed, and the correctness of the formula is proved. The experimental results show that the proposed algorithm is from tens to hundreds times faster than SN and roughly two times faster than SK when N increases, constructing a tree with 2 000 OTUs in 3 min on a current desktop computer. To earn the time with the cost of the space and reduce the computations in the innermost loop are the basic solutions for algorithms with many loops.

A simple way to visualize detailed phylogenetic tree of huge genome-wide SNP data constructed by SNPhylo

Phylogenetic trees based on genome-wide single nucleotide polymorphisms （SNPs） among diverse inbreds could provide valuable and intuitive information for breeding and germplasm management in crops. As a result of sequencing technology developments, a huge amount of whole genome SNP data have become available and affordable for breeders. However, it is a challenge to perform quick and reliable plotting based on the huge amount of SNP data. To meet this goal, a visualization pipeline was developed and demonstrated based on publicly available SNP data from the current important maize inbred lines, including temperate, tropical, sweetcorn, and popcorn. The detailed phylogenetic tree plotted by our pipeline revealed the authentic genetic diversity of these inbreds, which was consistent with several previous reports and indicated that this straightforward pipeline is reliable and could potentially speed up advances in crop breeding.

Using DNA Sequences and Phylogenetic Trees as Tools for Teaching Entomology to Undergraduate Students: A Simple Approach

This technical note aims to show how any instructor teaching entomology can use the Basic Local Alignment Search Tool (BLAST) and the “one click” mode of Phylogeny.fr to teach undergraduate students about insect DNA similarity in a simple way. Teaching an entomology course requires the use of numerous tools to help students grasp different concepts. Knowing that there are more than one million described species of insects means that teaching students about insect identification and taxonomy can be challenging. However, here we present two easy exercises that could be used as classroom or take-home assignments to demonstrate various levels of DNA similarity among different insect taxa. Such exercises unlock students’ creativity and break the barrier of fear of bioinformatics. Moreover, they open up new ways for them to understand insect taxonomy through molecular biology and allow them to develop new skills that contribute to strengthening their scientific performance in the future, especially when they do research as graduate students. Finally, this note is an example of how to integrate simple bioinformatics tools into the teaching of entomology.

LZ Complexity Distance of DNA Sequences and Its Application in Phylogenetic Tree Reconstruction

DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet （A, C, T, G）. As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals （Eutheria） with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.

PoInTree: A Polar and Interactive Phylogenetic Tree

PoInTree （Polar and Interactive Tree） is an application that allows to build, visualize, and customize phylogenetic trees in a polar, interactive, and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining （N J） algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynamically opened and closed and distances between genes are graphically represented. Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species. The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component （Steema software）.

Distances Between Phylogenetic Trees: A Survey

Phylogenetic trees have been widely used in the study of evolutionary biology for representing the tree-like evolution of a collection of species. However, different data sets and different methods often lead to the construction of different phylogenetic trees for the same set of species. Therefore, comparing these trees to determine similarities or, equivalently, dissimilarities, becomes the fundamental issue. Typically, Tree Bisection and Reconnection（TBR）and Subtree Prune and Regraft（SPR） distances have been proposed to facilitate the comparison between different phylogenetic trees. In this paper, we give a survey on the aspects of computational complexity, fixed-parameter algorithms, and approximation algorithms for computing the TBR and SPR distances of phylogenetic trees.

Partial Fusion (F) Gene Analysis of Newcastle Disease Virus Detected in Pakistan during 2021-2022

Newcastle disease (ND) virus is a leading threat to commercial and domestic poultry in Pakistan. The virus infects and constitutes irreversible impairment to the nervous system, damages the respiratory system, and marks severe gastrointestinal lesions leading to heavy mortality in short-living birds and substantial losses in layers and breeders. The continuous emergence and evolution of the virus made it inclined to evade the humoral response and indirectly the circumvention of artificial active immunization. Newcastle disease is caused by the orthoavula genus of the paramyxoviridae family and has shown high genetic diversity even in their genotypes while information regarding enzootic trends of the virus is scanty in Pakistan. A total of 40 tracheal samples of NDV were collected from different commercial broiler farms and 11 isolates of NDV were identified. In the current study, we determined the genetic diversity of the Newcastle disease virus based on the partial sequencing of the fusion protein gene available in the NCBI database. Genetic analysis showed that seven isolates belonged to class I genotype VII and four belonged to class II genotype II. Interestingly, two isolates had epidemiological connections with vaccine-like class II genotype II. Our findings, concerning the recent outbreaks of class I genotype VII and class II genotype II of NDV in vaccinated commercial flocks, suggest possible potential partial mutations in the fusion protein gene. Genetic diversity and formation of the new cleavage site in an important neutralizing protein of wild strain are linked with the potency of artificial active immunization and a major cause of vaccine failure.

Characterization of Avian Influenza A(H7N9) Virus Prevalence in Humans and Poultry in Huai′an,China：Molecular Epidemiology,Phylogenetic,and Dynamics Analyses

Objective To trace the source of human H7N9 cases in Huai＇an and elucidate the genetic characterization of Huai＇an strains associated with both humans and birds in live poultry market.Methods An enhanced surveillance was implemented when the first human H7N9 case was confirmed in Huai＇an.Clinical specimens,cloacal swabs,and fecal samples were collected and screened by real-time reverse transcription-polymerase chain reaction（RT-PCR） for H7N9 virus.The positive samples were subjected to further RT-PCR and genome sequencing.The phylodynamic patterns of H7N9 virus within and separated from Huai＇an and evolutionary dynamics of the virus were analyzed.Results Six patients with H7N9 infection were previously exposed to live poultry market and presented symptoms such as fever（〉38.0 °C） and headaches.Results of this study support the hypothesis that live poultry markets were the source of human H7N9 exposure.Phylogenetic analysis revealed that all novel H7N9 viruses,including Huai＇an strains,could be classified into two distinct clades,A and B.Additionally,the diversified H7N9 virus circulated in live poultry markets in Huai＇an.Interestingly,the common ancestors of the Huai＇an H7N9 virus existed in January 2012.The mean nucleotide substitution rates for each gene segment of the H7N9 virus were（3.09-7.26）×10-3 substitutions/site per year（95% HPD：1.72×10-3 to 1.16×10-2）.Conclusion Overall,the source of exposure of human H7N9 cases in Huai＇an was live poultry market,and our study highlights the presence of divergent genetic lineage of H7N9 virus in both humans and poultry specimens in Huai＇an.

Phylogenetic analysis and biological characteristic tests of marine bacteria isolated from Southern Ocean(Indian sector)water

Fifty-seven bacteria were isolated from Southern Ocean （Indian sector） water samples which were collected from different latitude and longitude of the ocean. All the isolates were able to grow at 4℃, 20℃, 37℃ and tolerable NaCI concentration up to 13.5% （w/v）. 29 out of 57 isolates were identified using 16S rDNA amplification and the sequences were submitted to National Center for Biotechnology Information （NCBI）. All the isolates were classified by using Ribosomal Database Project （RDP） and found that isolates belongs to Proteobacteria and Bacteriodes. The average G＋C content was 56.4%. The isolates were screened for the presence of extracellular enzymes, viz. amylase, catalase, urease, esterase, lipase and protease. The disc diffusion method is used to screen antibiotic production by the isolates against four pathogenic bacteria, viz. Salmonella typhimurium （NCIM 2501）, Staphylococcus aureus （NCIM 2122）, Bacillus subtilis （NCIM 2193）, and Pseudomonas aeruginosa （NCIM 2036）. Nine out of 29 were found to be antibiotic producer.

Classes of tree-based networks

Recently,so-called tree-based phylogenetic networks have attracted considerable attention.These networks can be constructed from a phylogenetic tree,called the base tree,by adding additional edges.The primary aim of this study is to provide sufficient criteria for tree-basedness by reducing phylogenetic networks to related graph structures.Even though it is generally known that determining whether a network is tree-based is an NP-complete problem,one of these criteria,namely edge-basedness,can be verified in linear time.Surprisingly,the class of edgebased networks is closely related to a well-known family of graphs,namely,the class of generalized series-parallel graphs,and we explore this relationship in full detail.Additionally,we introduce further classes of tree-based networks and analyze their relationships.

The complete genome of hydrocarbon-degrading Pseudoalteromonas sp. NJ289 and its phylogenetic relationship

Genus Pseudoalteromonas belongs to Family Pseudoalteromonadaceae in Gammaproteobacteria. A cold-adapted gram-negative bacterium, hydrocarbon-degrading Pseudoalteromonas sp. NJ289, was isolated from sea-ice of the Antarctica region, and sequenced the whole genome through the next generation sequencing platform. The assembly yielded three contigs representing two chromosomes and one plasmid with the sizes of 3.2 Mb, 636 kb and 1.8 kb, respectively. The G＋C contents of genome were 40.83% and included 3 589 ORFs. Functional annotation indicated some potential roles in enzymatic activity and environmental adaptability. This study may help for understanding the population diverse, evolutionary ecology and the microbial interaction.

Prevalence of cercarial infections in freshwater snails and morphological and molecular identification and phylogenetic trends of trematodes

Objective:To investigate the prevalence of cercarial infections in freshwater snails from several water sources in Nakhon Nayok,Nonthaburi,and Pathum Thani provinces of Central Thailand,and to reconstruct a phylogenetic tree for improved understanding of the relationships in the cercarial stage.Methods:The snail specimens were collected from 34 total sampling sites and investigated for cercarial infections using the crushing method.The cercarial specimens were classified and used for the phylogenetic tree analysis using the Internal Transcribed Spacer 2(ITS2).Results:A total of 1921 snail specimens were classified into five families and seven species.The results showed that four snail species were identified as intermediate hosts of the larval stages of trematodes,with an overall prevalence of infection of 2.45%(47/1921).The infected snail specimens included five groups of the cercarial type:cercariaeum cercariae,echinostome cercaria,megalurous cercaria,parapleurolophocercous cercaria,and xiphidiocercariae.This is particularly true of xiphidiocercariae,which was found to be the dominant type among cercarial infections in bithyniid snails by approximately 38.00%.With regard to molecular identification,the phylogenetic tree was reconstructed using the neighbor-joining method with 10000 bootstraps and separated the trematodes into three clades:Echinostomatoidea,Microphalloidea and Opisthorchioidea.Conclusions:The study reveals a high prevalence of cercarial infection for each cercarial type and maturation into a definite trematode genus and delineates morphological characteristics and evolutionary trends among each larval trematode in Nakhon Nayok,Nonthaburi and Pathum Thani provinces.In addition,the ITS2 sequence data of cercariae could be used to examine classification of these species at the family level.

Phylogenetic analysis of microRNA biomarkers for amyotrophic lateral sclerosis

Amnyotrophic lateral sderosis(ALS),also alled Lou Gchrig's disase,is an rreversible disase that is aused bythe degeneration and death of motor newons.Approximately 5-10%of cases are familial AIS(fALS),and the other cases are sporadic ALS(sALS).Gene mutations have been identifed both in fAIS and sALS patients.In this study,w disauss the four ALS-nelated genes,C9orf72,SODI,FUS,and TARDBP,and review the microRNAs(miRNAs)that are asociated with AlS and other neurological disordes from the litemature.A phylogentic analysis is used toexplore potential miRNAs that an be taken into acount when studying the dfference in pathology for AIS induced by the fowr genes and other ncurological discases such as frontotemporal dementia,spinal muscular atrophy,and narcolepsy.We found several miRNAs that an be taken into account to study the diference in pathology betwen AIS and other neurological disorders.

Study on Phylogenetic Relationships of Five Breeds of Pigs by Random Amplified Polymorphic DNA(RAPD)

RAPD was used to study the genetic divergency and phylogenetic relationships of five breeds of domestic pigs,including Min pig,Duroc,Yorkshired,Landrace and Junmu I pig.We selected fourteen primers from eighty random primers,caculated genetic distance index matrix and constructed phylogenetic tree with UPGMA methods.Genetic distance index matrix indicated that the genetic relationship between Junmu I pig and Landrace was the closest and the farthest between Duroc and min pig.

Phylogenetic analysis and in vitro culture of mosses fromthe Antarctic Fildes Peninsula

Molecular genetic techniques have proven very useful for initial analysis of the extent of genetic variation and dispersal in several Antarctic moss species. In the present study, the small subunit ribosomal RNA （SSU rDNA） and internal transcribed spacers of the nuclear ribosomal DNA （ITS rDNA） were sequenced in nine individuals of different mosses from the Fildes Peninsula of Antarctica. Sequence alignment showed that the extreme environment tended to increase the genetic diversity of Antarctic mosses. In addition, in our phylogenetic analysis, one previously unidentified Antarctic moss species was characterized by comparison with SSU and ITS rDNA sequences of known moss species. Moreover, the optimal culture medium and conditions for surface explant sterilization and protonemata induction in tissue culture of Pohlia nutans were investigated. The successful establishment of a tissue culture protocol together with the phylogenetic analysis of Antarctic mosses will provide technological support to establish an effective resource regeneration method for discovering new functional genes and gaining novel insights into the mechanisms of stress acclimation.

Phylogenetic Structure of Low Altitude Forest Communities in Baotianman Mountain

[Objectives]The paper was to reveal the phylogenetic structure of low altitude forest communities in Baotianman Mountain.[Methods]Ten 20 m×20 m plots were set at an altitude of 249-796 m in Baotianman Nature Reserve,in which 62 plant species were found.A phylogenetic tree was established on Phylomatic website,and the community related phylogenetic indexes at low altitude were calculated and analyzed,including net relatedness index(NRI),nearest taxon index(NTI),phylogenetic diversity Faith's PD index,phylogeneticβdiversity PhyloSor index and Dnn index.[Results]The NTI and NRI values of low altitude forest communities were generally greater than 0,showing phylogenetically clustered communities,and habitat filtration was the dominant factor in community construction.Combined with the species abundance matrix of plots,it was found that PD index had a significantly positive correlation with species richness.Phylogeneticβdiversity PhyloSor index was larger in the lower altitude area,which was exactly opposite to Dnn index.In other words,the more similar the community,the closer the distance between species,and the communities were phylogenetically clustered.[Conclusions]The study can provide a scientific basis for forest community management and restoration.

The Finding and Phylogenetic Evolution Analysis of Bovine Piroplasms in the Rasǒn Area of North Korea

The objective of this study was to investigate the epidemiology of bovine Piroplasms infections in the Rasǒn area of North Korea.The survey was carried out by light microscopic examination of Giemsa-stained blood smears,PCR,and phylogenetic evolution analysis of 128 blood samples collected from the Rasǒn area.The results showed that the infection rates of the small and large parasites were about 2.5 and 1.5% on average,respectively,in all Theileria sergenti and Babesia ovatapositive blood smears by microscopic examination of blood smears.The detection rate of T.sergenti Giemsa-stained smears was 43.75%,while that with PCR was 67.97%.The detection rate of B.ovata Giemsa-stained smears was 49.21%,while that with PCR was 71.88%.The sequence and phylogenetic analysis of DNA showed 98.84% homology between the 18S rRNA gene sequences of T.sergenti isolates from North Korean and that of Yanbian state from China,indicating the closest genetic relationship between both of them.Moreover,100% homology was shown between the 18S rRNA gene sequence of B.ovata isolates from North Korea and the published sequence AY081192 of GenBank,indicating the closest genetic relationship between both of them.This survey confirmed that Ras n is the endemic area of T.sergenti and B.ovata in North Korea.

Determination and Analysis of Mitochondrial ND2 Gene Sequence of Anas platyrhynchos

[Objective] The study was to analyze the phylogenesis of Anas platyrhynchos. [Method] Complete sequence of mitochondrial ND2 gene of 4 Anas platyrhynchos was determined by direct DNA sequencing based on PCR products. Combined with ND2 gene sequences of the Anas Linnaeus accessed in GenBank, phylogenetic tree was constructed by Neighbor-joining and maximum parsimony methods. [Result] The ND2 gene sequences of 4 Anas platyrhynchos were identical(1 041 bp in length; the nucleotide contents of A, G, T, and C were 28.91%, 13.35%, 20.75% and 36.98% respectively; A+T content approximated to that of C+G). Sequences of ND2 gene of mallard were same as spotbill duck, and had high homology with others. The phylogenetic trees indicated mallard and spotbilled duck were close in genetic relationship, both shared a haplotype; then Philippine duck, green-winged teal and northern pintail fell into branch ''A". [Conclusion] The domestic duck may be domesticated from mallard and spotbilled duck.

Plant F-Box Protein and Its Biological Function

F-box protein is an expanding family member of eukaryotic protein characterized by an F-box motif which has specificity of substrate recognition in the ubiquitin-mediated proteolysis.These proteins have been proved to be critical for many physiological processes,such as cell-cycle transition,signal transduction,gene transcription,male sterility,programmed cell death （PCD） and so on.This paper mainly introduces the biological functions of the known F-box proteins and the analysis of F-box gene phylogeny.

Molecular identification of hepatitis B virus genotypes/subgenotypes:Revised classification hurdles and updated resolutions

The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term “recombino-subgenotype”. Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term “immigro-subgenotype” to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.