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Related Concept Videos

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...
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,...
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...
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...
Survival Tree01:19

Survival Tree

Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
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Constructing a survival tree begins...

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A Practical Guide to Phylogenetics for Nonexperts
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Estimating trees from filtered data: identifiability of models for morphological phylogenetics.

Elizabeth S Allman1, Mark T Holder, John A Rhodes

  • 1Department of Mathematics and Statistics, University of Alaska Fairbanks, PO Box 756660, Fairbanks, AK 99775, USA.

Journal of Theoretical Biology
|December 17, 2009
PubMed
Summary

Stochastic models for phylogenetic inference are statistically consistent if parameters are identifiable. This study proves parameter identifiability for models of morphological characters with at least seven or eight leaves, depending on known tree topology.

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Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Stochastic models offer an alternative to parsimony analyses for phylogenetic inference using morphological characters.
  • These models account for ascertainment bias, observing only parsimony-informative characters.
  • Statistical consistency requires model parameter identifiability, an unaddressed issue.

Purpose of the Study:

  • To prove the identifiability of parameters for stochastic models of morphological characters.
  • To determine the minimum number of leaves required for parameter identifiability.
  • To investigate identifiability issues in four-taxon trees.

Main Methods:

  • Utilizing phylogenetic invariants to infer joint probabilities of parsimony-informative and non-informative patterns.
  • Analyzing models with finite state spaces of arbitrary size.
  • Examining identifiability based on the number of leaves in the phylogenetic tree.

Main Results:

  • Parameters are identifiable for models with at least eight leaves.
  • Identifiability is achieved with seven leaves if the tree topology is known.
  • Identifiability of the tree parameter fails for four-taxon trees.

Conclusions:

  • The study establishes conditions for the statistical consistency of model-based phylogenetic inference.
  • Identifiability of parameters is demonstrated for stochastic models under specific tree size constraints.
  • The findings provide a theoretical foundation for using these models in evolutionary studies.