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Sophisticated inferential tools coupled with the coalescent model have recently emerged for estimating past population sizes from genomic data. Recent methods that model recombination require small sample sizes, make constraining assumptions about population size changes, and do not report measures of uncertainty for estimates. Here, we develop a Gaussian… (More)

Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past population dynamics from genomic data. We start with a standard framework based on the coalescent, a stochastic process that… (More)

The goal of phylodynamics, an area on the intersection of phylogenetics and population genetics, is to reconstruct population size dynamics from genetic data. Recently, a series of nonparametric Bayesian methods have been proposed for such demographic reconstructions. These methods rely on prior specifications based on Gaussian processes and proceed by… (More)

Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past population dynamics from genomic data. We start with a standard framework based on the coalescent, a stochastic process that… (More)

MOTIVATION
The field of phylodynamics focuses on the problem of reconstructing population size dynamics over time using current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology but is particularly useful for studying the spread of quickly evolving infectious diseases agents, e.g.… (More)

Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting a coalescent model for the sampled individuals' genealogy and then integrating over all possible genealogies via Monte… (More)

We quantify the population divergence processes that shaped population genetic structure in the Trans-Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of southeastern Mexico. Multilocus genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to estimate the population divergence history for 47 samples of S.… (More)

We introduce phylodyn, an r package for phylodynamic analysis based on gene genealogies. The package's main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes several Markov chain Monte Carlo-based methods and an integrated nested Laplace approximation-based approach for… (More)

1 SplitHMC Here, we show how to solve Hamiltonian dynamics defined by (13) using the " splitting " strategy. Denote

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