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 se...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.展开更多
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...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 </span><span style="font-family:Verdana;">take-home assignments to demonstrate various levels of DNA similarity</span><span style="font-family:Verdana;"> 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. </span><span style="font-family:Verdana;">Finally, this note is an example of how to integrate simple bioinformatics </span><span style="font-family:Verdana;">tools into the teaching of entomology.展开更多
Understanding an underlying structure for phylogenetic trees is very important as it informs on the methods that should be employed during phylogenetic inference. The methods used under a structured population differ ...Understanding an underlying structure for phylogenetic trees is very important as it informs on the methods that should be employed during phylogenetic inference. The methods used under a structured population differ from those needed when a population is not structured. In this paper, we compared two supervised machine learning techniques, that is artificial neural network (ANN) and logistic regression models for prediction of an underlying structure for phylogenetic trees. We carried out parameter tuning for the models to identify optimal models. We then performed 10-fold cross-validation on the optimal models for both logistic regression?and ANN. We also performed a non-supervised technique called clustering to identify the number of clusters that could be identified from simulated phylogenetic trees. The trees were from?both structured?and non-structured populations. Clustering and prediction using classification techniques were?done using tree statistics such as Colless, Sackin and cophenetic indices, among others. Results from 10-fold cross-validation revealed that both logistic regression and ANN models had comparable results, with both models having average accuracy rates of over 0.75. Most of the clustering indices used resulted in 2 or 3 as the optimal number of clusters.展开更多
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 seque...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.展开更多
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...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).展开更多
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 c...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.展开更多
When microarray gene expression data are used to predict multiple drug resistance(MDR)phenotypes for anticancer drugs,the normalization strategy and the quality of the selected signature genes are usually the main cau...When microarray gene expression data are used to predict multiple drug resistance(MDR)phenotypes for anticancer drugs,the normalization strategy and the quality of the selected signature genes are usually the main causes of inconsistency among different experiments.A stable statistical drug response prediction model is urgently required in oncology.In this study,the microarray gene expression data of multiple cancer cell lines with MDR was analyzed.For each probe-set,the expression value was defined as present/absent(1/0)and was classified into a gene set defined with protein domain organization(PDO).After employing the gene content method of phylogenetic analysis,a phylogenetic model(cell tree)for MDR phenotype prediction was built at the PDO gene set level.The results indicate that classification of cancer cell lines is predominantly affected by both the histopa-thological features and the MDR phenotype(paclitaxel and vinblastine).When applying this model to predict the MDR phenotype of independent samples,the phylogenetic model performs better than signature gene models.Although the utility of our procedure is limited due to sample heterogeneity,it still has potential application in MDR research,especially for hematological tumors or established cell lines.展开更多
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 mar...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.展开更多
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 surveillanc...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.展开更多
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...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.展开更多
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 Anta...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.展开更多
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 t...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.展开更多
基金financially supported by the National Natural Science Foundation of China (31361140364)the National Major Project for Developing New GM Crops,Ministry of Agriculture,China (2016ZX080009-001)the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences to Xie Chuanxiao
文摘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.
文摘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 </span><span style="font-family:Verdana;">take-home assignments to demonstrate various levels of DNA similarity</span><span style="font-family:Verdana;"> 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. </span><span style="font-family:Verdana;">Finally, this note is an example of how to integrate simple bioinformatics </span><span style="font-family:Verdana;">tools into the teaching of entomology.
文摘Understanding an underlying structure for phylogenetic trees is very important as it informs on the methods that should be employed during phylogenetic inference. The methods used under a structured population differ from those needed when a population is not structured. In this paper, we compared two supervised machine learning techniques, that is artificial neural network (ANN) and logistic regression models for prediction of an underlying structure for phylogenetic trees. We carried out parameter tuning for the models to identify optimal models. We then performed 10-fold cross-validation on the optimal models for both logistic regression?and ANN. We also performed a non-supervised technique called clustering to identify the number of clusters that could be identified from simulated phylogenetic trees. The trees were from?both structured?and non-structured populations. Clustering and prediction using classification techniques were?done using tree statistics such as Colless, Sackin and cophenetic indices, among others. Results from 10-fold cross-validation revealed that both logistic regression and ANN models had comparable results, with both models having average accuracy rates of over 0.75. Most of the clustering indices used resulted in 2 or 3 as the optimal number of clusters.
基金supported by the National Natural Science Foundation of China(No.60371046).
文摘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.
文摘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).
基金supported by the National Natural Science Foundation of China (Nos.61103033,61173051, 61232001,and 70921001)
文摘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.
基金supported by the National High Technology Research and Development Program of China(2007AA02Z332,2008AA02Z126 and 2009AA02Z308)Shanghai Great Project Program Foundation(07DZ19505)
文摘When microarray gene expression data are used to predict multiple drug resistance(MDR)phenotypes for anticancer drugs,the normalization strategy and the quality of the selected signature genes are usually the main causes of inconsistency among different experiments.A stable statistical drug response prediction model is urgently required in oncology.In this study,the microarray gene expression data of multiple cancer cell lines with MDR was analyzed.For each probe-set,the expression value was defined as present/absent(1/0)and was classified into a gene set defined with protein domain organization(PDO).After employing the gene content method of phylogenetic analysis,a phylogenetic model(cell tree)for MDR phenotype prediction was built at the PDO gene set level.The results indicate that classification of cancer cell lines is predominantly affected by both the histopa-thological features and the MDR phenotype(paclitaxel and vinblastine).When applying this model to predict the MDR phenotype of independent samples,the phylogenetic model performs better than signature gene models.Although the utility of our procedure is limited due to sample heterogeneity,it still has potential application in MDR research,especially for hematological tumors or established cell lines.
文摘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.
基金supported by grants HAYf201516 from Huai’an Preventive Medicine Associationgrant HAS2015019-3 from Huai’an Scientific Technological Special Project
文摘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.
基金the Expedition support to MoES, New Delhi and NCAOR, Goa (No. Mo ES/NCAOR/SOS/1/2007-PC-I dated January 4, 2011)+5 种基金the Cumulative Professional Development Grant (CPDG Ref No. GO/PD/2011-12/269/3523 dated, August 04, 2011) from BIT, MesraBTISNet Sub DIC (BT/BI/065/2004) for providing internet facilities and the Government of JharkhandDepartment of Agriculture for providing infrastructure development fund (5/B.K.V/Misc/12/2001)the financial support as research fellowship to Centre of Excellence (COE) (Ref No. NPIU/TEQIP II/FIN/31/158, dated April 16, 2013) at the Department of BioEngineering
文摘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.
基金The National Natural Science Foundation of China under contract Nos 31200097,41576187,U1406402-5 and31202024the Basic Scientific Fund for National Public Research Institutes of China under contract Nos 2013G33 and 2015G10
文摘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.
基金funded by the state Mecklenburg-Western Pomerania by the Landesgraduierten-Studentshipfunded by the University of Greifswald by the Bogislaw-Studentshipfunded by the German Academic Scholarship Foundation by a studentship.
文摘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.