John Wakeley

A classification of structured coalescent processes with migration, conditional on the population pedigree

The paper extends coalescent models to account for pedigree effects in populations with subdivision and migration, finding pedigree effects in three out of four scenarios.

Latent mutations in the ancestries of alleles under selection

The paper analyzes the asymptotic behavior of latent mutations in a genetic locus under selection and mutation, showing that under certain conditions, the distribution of mutations matches the Ewens sampling formula.

Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture

This study evaluates qpAdm's performance in admixture analysis through simulations, finding it robust in many scenarios but cautioning against certain practices.

Bayesian Estimation of Population Size Changes by Sampling Tajima’s Trees

This paper introduces a Bayesian method called BESTT for inferring population size changes using Tajima’s coalescent, showing it is computationally efficient and accurate for both simulated and human data.

A non-zero variance of Tajima’s estimator for two sequences even for infinitely many unlinked loci

The paper shows Tajima’s estimator for two sequences has non-zero variance even with infinitely many unlinked loci due to correlations in coalescence times across loci.

Bayesian Nonparametric Inference of Population Size Changes from Sequential Genealogies

This paper introduces a Bayesian nonparametric method for inferring population size changes over time from genealogies, showing improved accuracy and uncertainty quantification compared to existing methods.