Impossibility of phylogeny reconstruction from $k$-mer counts

We consider phylogeny estimation under a two-state model of sequence evolution by site substitution on a tree. In the asymptotic regime where the sequence lengths tend to infinity, we show that for any fixed $k$ no statistically consistent phylogeny estimation is possible from $k$-mer counts over the full leaf sequences alone. Formally, we establish that the joint distribution of $k$-mer counts over the entire leaf sequences on two distinct trees have total variation distance bounded away from $1$ as the sequence length tends to infinity. Our impossibility result implies that statistical consistency requires more sophisticated use of $k$-mer count information, such as block techniques developed in previous theoretical work.

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