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What is the best argument for maximum parsimony method in phylogenetic tree construction?

1

$begingroup$

Beside it (maximum parsimony) being compuationally cheap what other good arguments are there for it? Is there any model behind this principle ? Why would one expect this principle to provide right phylogeny in any situation at all ?

phylogenetics phylogeny

share|improve this question

asked 15 hours ago

Ahmed AbdullahAhmed Abdullah

1776

$endgroup$

• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  You cross-posted this on Bio - cross-posting is discouraged across the SE network.
  $endgroup$
  – AliceD
  9 hours ago
  
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Noted. I didn't now that.
  $endgroup$
  – Ahmed Abdullah
  37 mins ago
  

  
  
  
  

add a comment | 

1

$begingroup$

Beside it (maximum parsimony) being compuationally cheap what other good arguments are there for it? Is there any model behind this principle ? Why would one expect this principle to provide right phylogeny in any situation at all ?

phylogenetics phylogeny

share|improve this question

asked 15 hours ago

Ahmed AbdullahAhmed Abdullah

1776

$endgroup$

• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  You cross-posted this on Bio - cross-posting is discouraged across the SE network.
  $endgroup$
  – AliceD
  9 hours ago
  
  
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Noted. I didn't now that.
  $endgroup$
  – Ahmed Abdullah
  37 mins ago
  

  
  
  
  

add a comment | 

$begingroup$

Beside it (maximum parsimony) being compuationally cheap what other good arguments are there for it? Is there any model behind this principle ? Why would one expect this principle to provide right phylogeny in any situation at all ?

phylogenetics phylogeny

share|improve this question

asked 15 hours ago

Ahmed AbdullahAhmed Abdullah

1776

$endgroup$

share|improve this question

asked 15 hours ago

Ahmed AbdullahAhmed Abdullah

1776

share|improve this question

asked 15 hours ago

Ahmed AbdullahAhmed Abdullah

1776

asked 15 hours ago

Ahmed AbdullahAhmed Abdullah

1776

asked 15 hours ago

Ahmed AbdullahAhmed Abdullah

1776

3 Answers
3

active

oldest

votes

2

$begingroup$

The principle of parsimony states that the simplest explanation consistent with a data set should be chosen over more complex explanations... (Stewart 1993)

Sometimes independent events in different lineages cause similarities in molecular sequences (or morphology or behavior or whatever characteristics one happens to be studying). These events are not true evidence of recently shared ancestry, but it is easy to mistake them as such evidence.

The principle of parsimony asserts that we will be better off assuming the simplest case--that is, that identical characters are evidence of recent shared ancestry, since the simple explanation should be true more frequently than alternative explanations. There are cases for which the maximum parsimony model works very well, and there are cases for which maximum likelihood, distance matrix, Bayesian, or other models perform better.

---

Stewart CB (1993) The powers and pitfalls of parsimony. Nature 361, 603-607, doi:10.1038/361603a0.

share|improve this answer

answered 13 hours ago

Daniel StandageDaniel Standage

2,890632

$endgroup$

• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Alot happened in phylogeny since 1993
  $endgroup$
  – Michael G.
  13 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  And yet the principle of parsimony remains the same, no?
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Not entirely sure what you mean, but parsimony is still parsimony and the fundamental idea of assessing a tree as an aggregate of every individual alignment position remains the same.
  $endgroup$
  – Michael G.
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  The OP asks why it even works at all, and my answer is that in some cases the simplest assumption is sufficient to infer the correct relationships. I don't see anything there that is compromised by the impressive advances in phylogeny inference that have occurred since.
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  I think you're mistaking me for a proponent of parsimony as opposed to someone trying to answer a question. :-) Don't worry, I was just as alarmed (and amused) several years ago when Cladistics announced it would only accept parsimony trees!
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  

 | 
show 1 more comment

2

$begingroup$

I'd say maximum parsimony approaches assume genetic similarity is unlikely to occur by convergence, but likely a result of divergence. If this assumptions holds, finding the tree configuration that minimizes the number of unlikely events makes sense.

share|improve this answer

answered 14 hours ago

PalliePallie

1906

$endgroup$

add a comment | 

1

$begingroup$

Parsimony was a nice idea and developed the algorithms and tree methods towards its successors, maximum likelihood and Bayesian. The fundamental assumption of mutational independence at each alignment position was founded via parsimony. Just the recursion algorithm involved in reading a tree isn't trivial coding. Also Walter Fitch (Fitch Marigold method) was a nice guy.

Weighted parsimony has performed well in simulation studies to prevent 'long branch attraction' artefacts. The key issue that was never resolved was how to objectively weight an MP analysis. It could be resurrected however, because machine learning ML could independently provide the weights in specific contexts. That a lot of "coulds" though.

share|improve this answer

answered 13 hours ago

Michael G.Michael G.

9551218

$endgroup$

add a comment | 

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2

$begingroup$

The principle of parsimony states that the simplest explanation consistent with a data set should be chosen over more complex explanations... (Stewart 1993)

Sometimes independent events in different lineages cause similarities in molecular sequences (or morphology or behavior or whatever characteristics one happens to be studying). These events are not true evidence of recently shared ancestry, but it is easy to mistake them as such evidence.

The principle of parsimony asserts that we will be better off assuming the simplest case--that is, that identical characters are evidence of recent shared ancestry, since the simple explanation should be true more frequently than alternative explanations. There are cases for which the maximum parsimony model works very well, and there are cases for which maximum likelihood, distance matrix, Bayesian, or other models perform better.

---

Stewart CB (1993) The powers and pitfalls of parsimony. Nature 361, 603-607, doi:10.1038/361603a0.

share|improve this answer

answered 13 hours ago

Daniel StandageDaniel Standage

2,890632

$endgroup$

• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Alot happened in phylogeny since 1993
  $endgroup$
  – Michael G.
  13 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  And yet the principle of parsimony remains the same, no?
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Not entirely sure what you mean, but parsimony is still parsimony and the fundamental idea of assessing a tree as an aggregate of every individual alignment position remains the same.
  $endgroup$
  – Michael G.
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  The OP asks why it even works at all, and my answer is that in some cases the simplest assumption is sufficient to infer the correct relationships. I don't see anything there that is compromised by the impressive advances in phylogeny inference that have occurred since.
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  I think you're mistaking me for a proponent of parsimony as opposed to someone trying to answer a question. :-) Don't worry, I was just as alarmed (and amused) several years ago when Cladistics announced it would only accept parsimony trees!
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  

 | 
show 1 more comment

2

$begingroup$

The principle of parsimony states that the simplest explanation consistent with a data set should be chosen over more complex explanations... (Stewart 1993)

Sometimes independent events in different lineages cause similarities in molecular sequences (or morphology or behavior or whatever characteristics one happens to be studying). These events are not true evidence of recently shared ancestry, but it is easy to mistake them as such evidence.

The principle of parsimony asserts that we will be better off assuming the simplest case--that is, that identical characters are evidence of recent shared ancestry, since the simple explanation should be true more frequently than alternative explanations. There are cases for which the maximum parsimony model works very well, and there are cases for which maximum likelihood, distance matrix, Bayesian, or other models perform better.

---

Stewart CB (1993) The powers and pitfalls of parsimony. Nature 361, 603-607, doi:10.1038/361603a0.

share|improve this answer

answered 13 hours ago

Daniel StandageDaniel Standage

2,890632

$endgroup$

• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Alot happened in phylogeny since 1993
  $endgroup$
  – Michael G.
  13 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  And yet the principle of parsimony remains the same, no?
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Not entirely sure what you mean, but parsimony is still parsimony and the fundamental idea of assessing a tree as an aggregate of every individual alignment position remains the same.
  $endgroup$
  – Michael G.
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  The OP asks why it even works at all, and my answer is that in some cases the simplest assumption is sufficient to infer the correct relationships. I don't see anything there that is compromised by the impressive advances in phylogeny inference that have occurred since.
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  


• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  I think you're mistaking me for a proponent of parsimony as opposed to someone trying to answer a question. :-) Don't worry, I was just as alarmed (and amused) several years ago when Cladistics announced it would only accept parsimony trees!
  $endgroup$
  – Daniel Standage
  12 hours ago
  

  
  
  
  

 | 
show 1 more comment

$begingroup$

The principle of parsimony states that the simplest explanation consistent with a data set should be chosen over more complex explanations... (Stewart 1993)

Sometimes independent events in different lineages cause similarities in molecular sequences (or morphology or behavior or whatever characteristics one happens to be studying). These events are not true evidence of recently shared ancestry, but it is easy to mistake them as such evidence.

The principle of parsimony asserts that we will be better off assuming the simplest case--that is, that identical characters are evidence of recent shared ancestry, since the simple explanation should be true more frequently than alternative explanations. There are cases for which the maximum parsimony model works very well, and there are cases for which maximum likelihood, distance matrix, Bayesian, or other models perform better.

---

Stewart CB (1993) The powers and pitfalls of parsimony. Nature 361, 603-607, doi:10.1038/361603a0.

share|improve this answer

answered 13 hours ago

Daniel StandageDaniel Standage

2,890632

$endgroup$

share|improve this answer

answered 13 hours ago

Daniel StandageDaniel Standage

2,890632

answered 13 hours ago

Daniel StandageDaniel Standage

2,890632

answered 13 hours ago

Daniel StandageDaniel Standage

2,890632

2

$begingroup$

I'd say maximum parsimony approaches assume genetic similarity is unlikely to occur by convergence, but likely a result of divergence. If this assumptions holds, finding the tree configuration that minimizes the number of unlikely events makes sense.

share|improve this answer

answered 14 hours ago

PalliePallie

1906

$endgroup$

add a comment | 

2

$begingroup$

I'd say maximum parsimony approaches assume genetic similarity is unlikely to occur by convergence, but likely a result of divergence. If this assumptions holds, finding the tree configuration that minimizes the number of unlikely events makes sense.

share|improve this answer

answered 14 hours ago

PalliePallie

1906

$endgroup$

add a comment | 

$begingroup$

I'd say maximum parsimony approaches assume genetic similarity is unlikely to occur by convergence, but likely a result of divergence. If this assumptions holds, finding the tree configuration that minimizes the number of unlikely events makes sense.

share|improve this answer

answered 14 hours ago

PalliePallie

1906

$endgroup$

share|improve this answer

answered 14 hours ago

PalliePallie

1906

answered 14 hours ago

PalliePallie

1906

answered 14 hours ago

PalliePallie

1906

1

$begingroup$

Parsimony was a nice idea and developed the algorithms and tree methods towards its successors, maximum likelihood and Bayesian. The fundamental assumption of mutational independence at each alignment position was founded via parsimony. Just the recursion algorithm involved in reading a tree isn't trivial coding. Also Walter Fitch (Fitch Marigold method) was a nice guy.

Weighted parsimony has performed well in simulation studies to prevent 'long branch attraction' artefacts. The key issue that was never resolved was how to objectively weight an MP analysis. It could be resurrected however, because machine learning ML could independently provide the weights in specific contexts. That a lot of "coulds" though.

share|improve this answer

answered 13 hours ago

Michael G.Michael G.

9551218

$endgroup$

add a comment | 

1

$begingroup$

Parsimony was a nice idea and developed the algorithms and tree methods towards its successors, maximum likelihood and Bayesian. The fundamental assumption of mutational independence at each alignment position was founded via parsimony. Just the recursion algorithm involved in reading a tree isn't trivial coding. Also Walter Fitch (Fitch Marigold method) was a nice guy.

Weighted parsimony has performed well in simulation studies to prevent 'long branch attraction' artefacts. The key issue that was never resolved was how to objectively weight an MP analysis. It could be resurrected however, because machine learning ML could independently provide the weights in specific contexts. That a lot of "coulds" though.

share|improve this answer

answered 13 hours ago

Michael G.Michael G.

9551218

$endgroup$

add a comment | 

$begingroup$

Parsimony was a nice idea and developed the algorithms and tree methods towards its successors, maximum likelihood and Bayesian. The fundamental assumption of mutational independence at each alignment position was founded via parsimony. Just the recursion algorithm involved in reading a tree isn't trivial coding. Also Walter Fitch (Fitch Marigold method) was a nice guy.

Weighted parsimony has performed well in simulation studies to prevent 'long branch attraction' artefacts. The key issue that was never resolved was how to objectively weight an MP analysis. It could be resurrected however, because machine learning ML could independently provide the weights in specific contexts. That a lot of "coulds" though.

share|improve this answer

answered 13 hours ago

Michael G.Michael G.

9551218

$endgroup$

share|improve this answer

answered 13 hours ago

Michael G.Michael G.

9551218

answered 13 hours ago

Michael G.Michael G.

9551218

answered 13 hours ago

Michael G.Michael G.

9551218