How can I interpret bootstrap values on phylogenetic trees built with Maximum Likelihood method?
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- The either do not resolve this particular bipartition at all (A and/or B are part of a soft polytomy) or produce a great variety of random bipartitions (e.g A but not B sister to C, D, E, F, G, H ...) all of which have frequencies of < 5% in the BS pseudo-replicate sample – this means: the sister relationship of A and B is supported by not perfect (somewhat faint) but coherent signal in the matrix.
- They consistently support a conflicting, alternative topology that places A as sister to C, which accordingly receives BS <= 30 — this means: part of your data prefers A as sister to B, but the other significant part prefers A as sister to C, you have internal signal conflict! And your tree only shows a part of the possible truth.
- 70% of your segregating sites are from maternally inherited genomes (plastome, mitochondriome), which are stronger affected by genetic drift and biogeography; 30% are from the biparentally inherited nucleome.
- Incomplete lineage sorting: part of your genes/data show different aspects of the true tree (or the coalescent).
- Combination of data with strongly differing evolutionary rates. The fast-evolving traits, genes may get the leaves right, but will be increasingly wrong towards the roots (saturation effects, branching artefacts); slow-evolving, conserved patterns can better resolve deep relationships but will not provide any support (or wrong support, when crucial data are missing due to sequencing gaps; ML is less vulnerable to this than MP or distance-based approaches) for the tip branches.
- All processes of evolutionary reticulation, hybridisation, introgression, lateral gene transfer etc (except for complete takeover by unilateral introgression) can express themselves in split BS support patterns.
- In the special application of palaeontology (morphological data sets including or exclusively compiled for extant organisms) actual ancestor-descendant relationships, or, in general, the overall level of primitiveness/derivedness. For instance: if A is the ancestor of B and C, and matrix perfectly reflects this situation, than both equally correct and wrong alternatives (A + B) + C and (A + C) + B will converge to BS = 50. In reality, the more primitive A and the more derived B and C, a third alternative A + (B + C) will also take its share. The faintness of coherent signal and actual ancestor-descendant relationships (old vs. young fossils vs. modern-day relatives) is the reason why palaeontological phylogenetic studies never get high levels of BS support (and if they do, it's either trivial relationships, when A is identical to B but different from anything else, BS ~ 100, or branching artefacts such as long-branch attraction)
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