Jointly Inferring the Dynamics of Population Size and Sampling Intensity from Molecular Sequences.

ABSTRACT: Estimating past population dynamics from molecular sequences that have been sampled longitudinally through time is an important problem in infectious disease epidemiology, molecular ecology, and macroevolution. Popular solutions, such as the skyline and skygrid methods, infer past effective population sizes from the coalescent event times of phylogenies reconstructed from sampled sequences but assume that sequence sampling times are uninformative about population size changes. Recent work has started to question this assumption by exploring how sampling time information can aid coalescent inference. Here, we develop, investigate, and implement a new skyline method, termed the epoch sampling skyline plot (ESP), to jointly estimate the dynamics of population size and sampling rate through ti

SUBMITTER: Parag KV 

PROVIDER: S-EPMC7403618 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature