Title: Identifiability of phylogenetic parameters from k-mer data under the coalescent,
Abstract: Distances between sequences based on their $k$-mer frequency counts can be
used to reconstruct phylogenies without first computing a sequence alignment.
Past work has shown that effective use of k-mer methods depends on 1)
model-based corrections to distances based on $k$-mers and 2) breaking long
sequences into blocks to obtain repeated trials from the sequence-generating
process. Good performance of such methods is based on having many high-quality
blocks with many homologous sites, which can be problematic to guarantee a
priori.
Nature provides natural blocks of sequences into homologous regions---namely,
the genes. However, directly using past work in this setting is problematic
because of possible discordance between different gene trees and the underlying
species tree. Using the multispecies coalescent model as a basis, we derive
model-based moment formulas that involve the divergence times and the
coalescent parameters. From this setting, we prove identifiability results for
the tree and branch length parameters under the Jukes-Cantor model of sequence
mutations.