Median Networks

Speedy Construction and Greedy Reduction, One Simulation, and Two Case Studies from Human mtDNA

Hans Jürgen Bandelt, Vincent Macaulay, Martin Richards

Research output: Contribution to journalArticle

163 Citations (Scopus)

Abstract

Molecular data sets characterized by few phylogenetically informative characters with a broad spectrum of mutation rates, such as intraspecific control-region sequence variation of human mitochondrial DNA (mtDNA), can be usefully visualized in the form of median networks. Here we provide a step-by-step guide to the construction of such networks by hand. We improve upon a previously implemented algorithm by outlining an efficient parametrized strategy amenable to large data sets, greedy reduction, which makes it possible to reconstruct some of the confounding recurrent mutations. This entails some postprocessing as well, which assists in capturing more parsimonious solutions. To simplify the creation of the resulting network by hand, we describe a speedy approach to network construction, based on a careful planning of the processing order. A coalescent simulation tailored to human mtDNA variation in Eurasia testifies to the usefulness of reduced median networks, while highlighting notorious problems faced by all phylogenetic methods in this context. Finally, we discuss two case studies involving the comparison of characters in the two hypervariable segments of the human mtDNA control region in the light of the worldwide control-region sequence database, as well as additional restriction fragment length polymorphism information. We conclude that only a minority of the mutations that hit the second segment occur at sites that would have a mutation rate comparable to those at most sites in the first segment. Discarding the known 'noisy' sites of the second segment enhances the analysis. 

Original languageEnglish
Pages (from-to)8-28
Number of pages21
JournalMolecular Phylogenetics and Evolution
Volume16
Issue number1
DOIs
Publication statusPublished - Jul 2000
Externally publishedYes

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Mitochondrial DNA
mitochondrial DNA
mutation
Mutation Rate
case studies
Hand
simulation
Mutation
hands
Restriction Fragment Length Polymorphisms
Case-Control Studies
Eurasia
Databases
restriction fragment length polymorphism
polymorphism
planning
phylogenetics
phylogeny
Datasets
rate

Cite this

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abstract = "Molecular data sets characterized by few phylogenetically informative characters with a broad spectrum of mutation rates, such as intraspecific control-region sequence variation of human mitochondrial DNA (mtDNA), can be usefully visualized in the form of median networks. Here we provide a step-by-step guide to the construction of such networks by hand. We improve upon a previously implemented algorithm by outlining an efficient parametrized strategy amenable to large data sets, greedy reduction, which makes it possible to reconstruct some of the confounding recurrent mutations. This entails some postprocessing as well, which assists in capturing more parsimonious solutions. To simplify the creation of the resulting network by hand, we describe a speedy approach to network construction, based on a careful planning of the processing order. A coalescent simulation tailored to human mtDNA variation in Eurasia testifies to the usefulness of reduced median networks, while highlighting notorious problems faced by all phylogenetic methods in this context. Finally, we discuss two case studies involving the comparison of characters in the two hypervariable segments of the human mtDNA control region in the light of the worldwide control-region sequence database, as well as additional restriction fragment length polymorphism information. We conclude that only a minority of the mutations that hit the second segment occur at sites that would have a mutation rate comparable to those at most sites in the first segment. Discarding the known 'noisy' sites of the second segment enhances the analysis. ",
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Median Networks : Speedy Construction and Greedy Reduction, One Simulation, and Two Case Studies from Human mtDNA. / Bandelt, Hans Jürgen; Macaulay, Vincent; Richards, Martin.

In: Molecular Phylogenetics and Evolution, Vol. 16, No. 1, 07.2000, p. 8-28.

Research output: Contribution to journalArticle

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