What is the best argument for maximum parsimony method in phylogenetic tree construction? ...
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What is the best argument for maximum parsimony method in phylogenetic tree construction?
Announcing the arrival of Valued Associate #679: Cesar Manara
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$begingroup$
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
asked 15 hours ago
Ahmed AbdullahAhmed Abdullah
1776
$endgroup$
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
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
asked 15 hours ago
Ahmed AbdullahAhmed Abdullah
1776
$endgroup$
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
phylogenetics phylogeny
asked 15 hours ago
Ahmed AbdullahAhmed Abdullah
1776
asked 15 hours ago
Ahmed AbdullahAhmed Abdullah
1776
asked 15 hours ago
Ahmed AbdullahAhmed Abdullah
1776
asked 15 hours ago
Ahmed AbdullahAhmed Abdullah
1776
asked 15 hours ago
Ahmed AbdullahAhmed Abdullah
1776
1776
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
$begingroup$
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
1
1
$begingroup$
You cross-posted this on Bio - cross-posting is discouraged across the SE network.
$endgroup$
– AliceD
9 hours ago
$begingroup$
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
$begingroup$
Noted. I didn't now that.
$endgroup$
– Ahmed Abdullah
37 mins ago
add a comment |
3 Answers
3
active
oldest
votes
$begingroup$
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.
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
$begingroup$
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.
answered 14 hours ago
PalliePallie
1906
$endgroup$
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.
answered 13 hours ago
Michael G.Michael G.
9551218
$endgroup$
add a comment |
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3 Answers
3
active
oldest
votes
3 Answers
3
active
oldest
votes
active
oldest
votes
active
oldest
votes
$begingroup$
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.
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.
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.
answered 13 hours ago
Daniel StandageDaniel Standage
2,890632
$endgroup$
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.
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
answered 13 hours ago
Daniel StandageDaniel Standage
2,890632
2,890632
$begingroup$
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
$begingroup$
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
$begingroup$
Alot happened in phylogeny since 1993
$endgroup$
– Michael G.
13 hours ago
$begingroup$
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
$begingroup$
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
$begingroup$
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
$begingroup$
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
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
$begingroup$
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
$begingroup$
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.
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.
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.
answered 14 hours ago
PalliePallie
1906
$endgroup$
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.
answered 14 hours ago
PalliePallie
1906
answered 14 hours ago
PalliePallie
1906
answered 14 hours ago
PalliePallie
1906
answered 14 hours ago
PalliePallie
1906
1906
add a comment |
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.
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.
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.
answered 13 hours ago
Michael G.Michael G.
9551218
$endgroup$
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.
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
answered 13 hours ago
Michael G.Michael G.
9551218
9551218
add a comment |
add a comment |
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$begingroup$
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