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Related Concept Videos

Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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A Practical Guide to Phylogenetics for Nonexperts
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Published on: February 5, 2014

PhyloPars: estimation of missing parameter values using phylogeny.

Jorn Bruggeman1, Jaap Heringa, Bernd W Brandt

  • 1Department of Theoretical Biology, Faculty of Earth & Life Sciences, VU University Amsterdam, The Netherlands. jorn.bruggeman@falw.vu.nl

Nucleic Acids Research
|May 16, 2009
PubMed
Summary
This summary is machine-generated.

PhyloPars infers metabolic parameters for species using evolutionary relationships and incomplete data. This method accurately estimates missing values, aiding systems biology and ecology research.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Metabolic parameters of a species can be inferred from related species using phylogenetic information.
  • Phylogenetic data complements empirical evidence, especially when experiments are not feasible.
  • Accurate metabolic parameter estimation is crucial for fields like systems biology and ecology.

Purpose of the Study:

  • To develop a statistically consistent method for estimating metabolic parameters using incomplete empirical observations and species phylogeny.
  • To create a web server (PhyloPars) that combines evolutionary models with missing data handling for comprehensive parameter estimation.
  • To provide accurate metabolic parameter estimates that are an order of magnitude more precise than traditional methods.

Main Methods:

  • Utilizing a state-of-the-art evolutionary model extended to handle missing data.
  • Combining incomplete empirical observations with species phylogeny to generate complete parameter estimates.
  • Implementing real-time cross-validation to assess the accuracy and bias of estimated values.

Main Results:

  • The PhyloPars web server provides statistically consistent estimates for all species, even with incomplete data.
  • The approach optimally uses all available information, yielding estimates significantly more accurate than ad-hoc alternatives.
  • Users can obtain estimates of missing metabolic values with a measure of certainty by uploading a phylogeny and feature matrix.

Conclusions:

  • PhyloPars offers an efficient and easy-to-use method for estimating metabolic parameters.
  • The tool leverages phylogenetic relationships and incomplete data for robust predictions.
  • This approach has broad applicability, benefiting systems biology, ecology, and related scientific fields.