Answers.Body: <p>No. A perfect phylogeny is one such that all characters evolve on the tree with no homoplasy, i.e. for a binary character, changes occur once from 0 -&gt; 1 but never from 1 -&gt; 0. Maximum parsimony inference <em>may</em> produce a perfect phylogeny, but typically for real datasets some degree of homoplasy is required to explain character patterns.</p>
  
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Answers.Body: <p>Long discussion that took many years to resolve. </p>
  
  <p>MP doesn't account for back mutation, which is a HUGE problem for nucleotide data because in theory 1:4 mutations is a back mutation. Maximum likelihood has resumed is crown here, however Beast deployment of a Bayesian calculation is also very widely, particularly for molecular dating. ML uses  a reversible matrix A &lt;-> T, whilst Beast uses a directional matrix A->T and will score T->A separately.</p>
  
  <p>Happy to discuss the approaches and modern interpretations at length.</p>
  
  <p>The model which accounts for back-mutation is the Jukes-Cantor correction (JC correction), this is a basic model present in every phylogenetic algorithm except p-distances). Essentially JC extrapolates back-calculation for the true number of mutations against the observed number of mutations against divergence time. However, when the P-distance (uncorrected observed distance) exceeds 0.75 for nucleotides the model is not viable. Basically, nucleotide divergence >0.75 is saturated and the phylogenetic information is essentially random.</p>
  
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Answers.Text: Imo a general comment about phylogenetic methods is not particularly helpful for the distinction between most MP trees and one that mathematically fits the description of a perfect phylogeny. But to which models are you referring to for ML and BEAST? AFAIK they have consistent sets of CTMC models.
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Body: <p>I am searching various sources about phylogenetics. I saw some materials about <a href="https://en.wikipedia.org/wiki/Perfect_phylogeny" rel="nofollow noreferrer">perfect phylogeny</a> and also phylogenies acquired from <a href="https://en.wikipedia.org/wiki/Maximum_parsimony_(phylogenetics)" rel="nofollow noreferrer">maximum parsimony</a> constraint. They seem very similar to me. Are they the same?</p>
  
Tags: <phylogenetics><ngs><phylogeny>
Title: Perfect Phylogeny vs Maximum parsimony
ThreadText: # Perfect Phylogeny vs Maximum parsimony
  
  (Asked by: username_0 on 2019-02-04)
  
  I am searching various sources about phylogenetics. I saw some materials about [perfect phylogeny](https://en.wikipedia.org/wiki/Perfect_phylogeny) and also phylogenies acquired from [maximum parsimony](https://en.wikipedia.org/wiki/Maximum_parsimony_(phylogenetics)) constraint. They seem very similar to me. Are they the same?
  
  **Tags:** phylogenetics, ngs, phylogeny
  
  
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  ## 2 answers
  
  ### Answer by username_1 on 2019-02-04. Score: 3 | Accepted answer
  
  No. A perfect phylogeny is one such that all characters evolve on the tree with no homoplasy, i.e. for a binary character, changes occur once from 0 -> 1 but never from 1 -> 0. Maximum parsimony inference *may* produce a perfect phylogeny, but typically for real datasets some degree of homoplasy is required to explain character patterns.
  
  
  ---
  
  ### Answer by username_2 on 2019-02-04. Score: 2
  
  Long discussion that took many years to resolve.
  
  MP doesn't account for back mutation, which is a HUGE problem for nucleotide data because in theory 1:4 mutations is a back mutation. Maximum likelihood has resumed is crown here, however Beast deployment of a Bayesian calculation is also very widely, particularly for molecular dating. ML uses a reversible matrix A <-> T, whilst Beast uses a directional matrix A->T and will score T->A separately.
  
  Happy to discuss the approaches and modern interpretations at length.
  
  The model which accounts for back-mutation is the Jukes-Cantor correction (JC correction), this is a basic model present in every phylogenetic algorithm except p-distances). Essentially JC extrapolates back-calculation for the true number of mutations against the observed number of mutations against divergence time. However, when the P-distance (uncorrected observed distance) exceeds 0.75 for nucleotides the model is not viable. Basically, nucleotide divergence >0.75 is saturated and the phylogenetic information is essentially random.
  
  > **Comments:**
  > **username_1**: Imo a general comment about phylogenetic methods is not particularly helpful for the distinction between most MP trees and one that mathematically fits the description of a perfect phylogeny. But to which models are you referring to for ML and BEAST? AFAIK they have consistent sets of CTMC models.  
  
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