<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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2019-02-04T12:34:35.850Z
2023-08-15T11:27:34.123Z
2023-08-15T11:27:34.123Z
NatWH
<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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2019-02-04T14:31:17.083Z
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.
NatWH
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2019-02-04T13:29:21.850Z
2019-02-04T16:31:03.863Z
2019-02-04T16:31:03.863Z
M__
<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>

<phylogenetics><ngs><phylogeny>
Perfect Phylogeny vs Maximum parsimony
# 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.


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### 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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