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What do the bootstrap values indicate about the relationship between the species? I'm working on Mega program but I don;t understand what bootstrap value means in simple terms and also what does it indicate about the relationship between species

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    $\begingroup$ Welcome to Biology.SE! What research have you done before asking it here? $\endgroup$ – another 'Homo sapien' Jul 15 '17 at 14:45
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The bootstrap values belong to a wide category of values called support values. Support values in general are used to give some indication of the degree to which one can be confident that the branch represents some "signal" present in the data.

In particular, bootstrap values indicate how robust the branches in the tree are, that is, how resistant they are to perturbation in the data. They are obtained by re-sampling columns in the data matrix, building trees from such re-sampled matrices, and looking at the proportion of the obtained trees that contain a given branch.

In the case of bootstrap, the re-sampling step is done the following way: Suppose that the original data matrix has N columns (i.e. N encoded characters, that can be nucleotides or amino-acids in an sequence alignment, morphological characters, presence-absence of genomic features, etc.). A new matrix will be obtained by randomly drawing one of these columns, N times. The new matrix will therefore have the same number of characters, but some from the original matrix will be present multiple times and some will be absent. This will influence the topology of the tree. For instance, if a branch was supported by characters that now are absent, this branch may not appear any more with this particular re-sampling. The re-sampling is usually done around 100 or 1000 times.

A low bootstrap value means that if the tree is built using a subset of the data, it is likely that this branch will not appear.

A high bootstrap value means that the branch will likely appear on a tree built from such a re-sampled matrix. This does not necessarily mean that the branch is more likely to represent the true historical relationships, though: sometimes, reconstruction artifacts can be robust. For instance, with some molecular phylogeny reconstruction methods, taxa may end up being grouped based on similarities in genome composition. High bootstrap values indicate that there is a strong signal in the data supporting the branch, be it historical signal or other.

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  • $\begingroup$ Nice answer +1. Would you mind clarifying how we resample. Just explaining how are the data organized in the matrix might help to clarify what re-sampling columns in the data matrix really mean. Does it mean subsetting the SNPs sequenced, or the individuals available, or some other pre-processed statistics, etc...? $\endgroup$ – Remi.b Jul 25 '17 at 16:50
  • $\begingroup$ @Remi.b I tried to expand a little my answer. This is re-sampling of characters (conventionally encoded as columns), not individuals (conventionally encoded as lines). Note that re-sampling of individuals would lead to trees on different sets of taxa, and it would therefore be impossible to simply compare branches between trees and compute branch support values. $\endgroup$ – bli Jul 25 '17 at 17:11
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    $\begingroup$ @Remi.b If you can read French and are interested in these support values thing, you may have a look at the introduction of my thesis (pages 9 and 10 of tel.archives-ouvertes.fr/tel-00331825). I see that I mentioned "perturbations de l’échantillonnage taxinomique" in ways of measuring robustness, but I can't remember what I had in mind... $\endgroup$ – bli Jul 25 '17 at 17:24
  • $\begingroup$ Wow I did not know people are still writing PhD thesis in french! It feels like a pain having to translate your publications from english to french just for the thesis. Yes, I can read french. Thanks for the link. $\endgroup$ – Remi.b Jul 25 '17 at 17:38
  • $\begingroup$ In France, I think it is still pretty common to write theses in French (especially in humanities, but not only). The main text of the thesis was written in French, but the articles were included as is, in English. I'm happy I could write in my mother tongue: it made the experience much more enjoyable. $\endgroup$ – bli Jul 25 '17 at 17:47

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