The single main root of phylogenetics is Hennig's reformulation of the comparative method, but the empirical basis has increased enormously in recent years with the availability of an exponentially increasing amount of molecular sequence data, to be analysed through increasingly sophisticated algorithms. Progress has been overcoming the pitfalls of earlier naïve hypotheses, such as the putatively uniform rate of the molecular clock across lineages, as well as problems deriving from gene duplication, gene loss, and horizontal gene transfer. However, the intrinsic limits of the resolution power of sequence comparisons are also emerging, as in the case of geologically old sequences of a series of branchings of the phylogenetic tree, which reduce in practice to multibranched star-shaped phylogenies. The single best source of data for the molecular phylogeny of the Metazoa is arguably the mitochondrial genome, in terms of gene, genome sequences, and also gene order
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