Information on hidden birth events restores identifiability in phylodynamic inference

TL;DR

This paper demonstrates that incorporating information on hidden birth events and mutation accumulation at birth can restore parameter identifiability in complex phylodynamic models.

Contribution

It shows that parameter identifiability in birth-death models can be achieved with additional data on hidden events and mutations, even in time-dependent scenarios.

Findings

Parameter identifiability is restored with hidden birth event data.

Mutation accumulation at birth makes all parameters identifiable.

Identifiability holds for models with time-dependent rates and sampling schemes.

Abstract

The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter identifiability can be recovered even for the most general cases of time-dependent rates when additional information on hidden birth events along branches of the reconstructed tree is available. This holds both for models in which individuals are sampled at a single point in time or through time at a time-dependent rate. Moreover, we prove that when mutations occur at birth - assuming two different models for the accumulation of mutations at a birth event - then information about hidden birth events is available in the sequences and thus all parameters of time-dependent birth-death models become identifiable. Thus, phylodynamic inference is identifiable whenever evolutionary models with mutation accumulation at birth (such as at speciation, transmission, or cell division) are plausible.