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Repeatedly in recent years, phylogenetic analyses of linguistic data have reached the world's leading scientific journals, but in ways hugely controversial within linguistics itself. Phylogenetic analysis methods, taken from the biological sciences, have been applied to date and track how major language families dispersed through prehistory, with implications also for archaeology and genetics. As this approach is extended to ever more language families worldwide, this review offers methodological perspectives and cautionary tales from the most high-profile and hotly disputed case of all: Indo-European. This article surveys the checkered history of these phylogenetic methods and of the cognacy databases they have relied on for their linguistic input data. It clears up cross-disciplinary misconceptions about this new methodology, identifies major flaws in the current state of the art (hence its highly inconsistent results), diagnoses the causes, and outlines new solutions that might bring the field closer to living up to its potential.
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