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Phylogenetic systematics seeks to describe and reconstruct the evolutionary relationships among and between organisms making use of molecular data. This field has become immensely popular in recent years, with the associated computational demands growing in leaps and bounds. Here, we review the progress made in statistical phylogenetics, compare the various methods and highlight the recent trends and pitfalls. Furthermore, we delve into the mathematical models associated with these methods to understand the underlying assumptions, while tracking the improvements made. Lastly, we look at the impact and use of phylogenetics in ecology.