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Genetic Drift

Natural selection—probably the most well-known evolutionary mechanism—increases the prevalence of traits that enhance survival and reproduction. However, evolution does not merely propagate favorable traits, nor does it always benefit populations.Life is not fair. A deer grazing contentedly in a field can have her meal cut tragically short by a bolt of lightning. If the doomed doe is one of only three in the population, 1/3 of the population’s gene pool is lost. Random events like this can...
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Development of an Individual-Tree Basal Area Increment Model using a Linear Mixed-Effects Approach
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Shrinkage effect in ancestral maximum likelihood.

Elchanan Mossel1, Sebastien Roch, Mike Steel

  • 1Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, CA 94720-3860, USA. mossel@stat.berkeley.edu

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|January 31, 2009
PubMed
Summary
This summary is machine-generated.

Ancestral maximum likelihood (AML) is statistically inconsistent, unlike standard maximum likelihood (ML) phylogenetic methods. This study proves AML can inaccurately resolve evolutionary trees by shrinking short branches as sequence data increases.

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Area of Science:

  • Computational Biology
  • Phylogenetics
  • Evolutionary Biology

Background:

  • Ancestral maximum likelihood (AML) reconstructs phylogenetic trees and ancestral sequences.
  • AML optimizes trees and sequences using a Markov model with shared branch lengths.
  • It differs from maximum likelihood (ML) by not averaging over all possible ancestral sequences.

Purpose of the Study:

  • To formally determine the statistical consistency of AML.
  • To investigate the implications of AML's statistical properties on phylogenetic reconstruction.

Main Methods:

  • Theoretical analysis of AML under a Markov model of sequence evolution.
  • Mathematical proof demonstrating the statistical properties of AML with varying sequence lengths.

Main Results:

  • AML is statistically inconsistent, contrary to previous assumptions.
  • AML can lead to the 'shrinking' of short phylogenetic branches.
  • This shrinking results in a loss of internal resolution in reconstructed trees as sequence length increases.

Conclusions:

  • AML is not statistically consistent and can produce inaccurate phylogenetic trees.
  • The method's limitations impact its reliability for reconstructing evolutionary history.
  • Researchers should be cautious when using AML for phylogenetic inference, especially with long sequences.