Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks

Bryant, David; Moulton, Vincent

doi:10.1093/molbev/msh018

Cited by 1,687 publications

(1,204 citation statements)

References 49 publications

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“…Since the snRNA sequences are short and in addition there are several highly variable regions, we use split decomposition [1] and the neighbor net [7] algorithm (as implemented as part of the SplitsTree4 package [33]) to construct phylogenetic networks rather than phylogenetic trees. The advantage of these method is that they are very conservative and that the reconstructed networks provide and easy-tograsp representation of the considerable noise in the sequence data.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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While studies of the evolutionary histories of protein families are common place, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the 9 spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely or partially sequenced genomes of metazoan animals. Representatives of the five major spliceosomal snRNAs were found in all genomes. None of the minor splicesomal snRNAs was detected in Nematodes and in the shotgun traces of Oikopleura dioica, while in all other animal genomes at most one of them is missing. Although snRNAs are present in multiple copies in most genomes, distinguishable paralog groups are not stable over long evolutionary times, although they appear independently in several clades. In general, animal snRNA secondary structures are highly conserved, albeit in particular U11 and U12 in insects exhibit dramatic variations. An analysis of genomic context of snRNAs reveals that they behave like mobile elements, exhibiting very little syntenic conservation.

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Section: Phylogenetic Analysismentioning

confidence: 99%

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

2008

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“…The combinatorial use of different markers along with different computational tools, ideally the use of NeighborNet algorithm 42 , takes a different approach to inferring species relationships. A relationship network is drawn rather than restricting the data into a stubborn single line tree structure by incorporating MP trees onto a ML tree.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny and biogeography of the carnivorous plant family Droseraceae with representative Drosera species from Northeast India

et al. 2017

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“…For example, it can use an annotated reference genome as the source of comparison sequences to BLAST against other genomes in the database. This generates whole-genome profiles that can be analysed by standard distance methods such as NeighbourNet 73 implemented within the SplitsTree package 74 , simultaneously providing lists of loci that are identical, variable, missing or truncated (incomplete genes located at the ends of contigs) among data sets. BIGSdb allows queries through web-based interfaces, making annotated genome content accessible to external databases and analysis software as well as to users querying the data directly (FIG.…”

Section: Gene-by-gene Typing Infrastructurementioning

confidence: 99%

MLST revisited: the gene-by-gene approach to bacterial genomics

et al. 2013

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Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.Advances in nucleotide-sequencing technology have provided unparalleled access to the enormous genetic diversity that has accumulated in the bacterial domain during 3.5-4 billion years of evolution 1 . Numerous sets of whole-genome sequencing (WGS) data for bacterial isolates (BOX 1) are available 2 , and metagenomic studies using these technologies continue to reveal further, seemingly boundless, diversity in bacterial communities 3 . Faced with this plethora of information, microbiologists must develop structured means of describing this diversity and of linking phenotype and genotype, thereby facilitating an improved understanding of the microbiological world. Given that we have precise information on the function of only a very small proportion of bacterial genes, and no knowledge at all about most, this is a formidable, if extremely exciting, challenge.Here, we focus primarily on pathogenic bacteria, although the concepts discussed are applicable more widely to all bacteria and archaea. Bacterial pathogens played a crucial part in the development of experimental microbiology and remain the most intensively studied prokaryotes more than 100 years later 4 . Pathogens have emerged across the diversity of the bacterial -but, interestingly, not the archaeal -domain on many occasions and are both polyphyletic and highly diverse. Thus, although pathogens represent only a tiny subset of the bacterial world, the challenges faced by the clinical microbiology laboratory are representative of those faced by microbiology as a whole.Taxonomic and functional analyses are based on the observations that diversity among bacteria is not continuous and that distinct, stable types with particular properties exist 5 . These founding principles of microbiology 6 have been upheld by much subsequent research, but the study of such clusters remains largely descriptive, and the evolutionary mechanisms that led to cluster emergence and persistence remain incompletely understood 7,8 . Structuring is also evident within bacterial genomes, as diversity is unevenly distributed among genes Pre-WGS cataloguing of diversityA major advance in defining bacterial diversity was the proposal, by the late Carl Woese and colleagues, of a universal and 'natural' -that is, genealogical -classification system based on small-su...

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Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks

Cited by 1,687 publications

References 49 publications

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Phylogeny and biogeography of the carnivorous plant family Droseraceae with representative Drosera species from Northeast India

MLST revisited: the gene-by-gene approach to bacterial genomics

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