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Generally speaking, heterochromatin or euchromatin structures mark specific regions to regulate the transcriptional activity and these marks carry the signature of developmental processes as they differ in different tissues (or cell types). Therefore, we should not ignore the developmental processes if we want to understand how such epigenetic marks are ...


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You might want to have a look at some of these: Patterns of speciation and limits to phylogenetic resolution, Molecular polytomies, Problems with "soft" polytomies, and Polytomies, the power of phylogenetic inference, and the stochastic nature of molecular evolution.


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I think that changes in features that determine a node may happen in parallel or close together in a sequence. If the fossil record is not complete enough then the cladogram has to contain these stars. From a stochastic statistic point of view, although unlikely, it could actually happen that 2 or more characteristics develop exactly during a similar time ...



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