# Raw-Data – HIV-1 Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection

This archive contains the data used in the manuscript "HIV-1 Simulation
Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate
Estimates Under Selection". This archive can be used in conjunction with
the code repository to reproduce the data analysis.

## Abstract

Phylodynamic methods are widely used to infer the population dynamics of
viruses between and within hosts. For HIV-1, these methods have been used to
estimate migration rates between different anatomical compartments within a
host. These methods typically assume that the genomic regions used for
reconstruction are evolving without selective pressure, even though other
parts of the viral genome are known to experience strong selection. In this
study, we investigate how selection affects phylodynamic migration rate
estimates. To this end, we developed a novel agent-based simulation tool,
`virolution`, to simulate the evolution of virus within two anatomical
compartments of a host. Using this tool, we generated viral sequences and
genealogies assuming both, neutral evolution and purifying selection that is
concordant in both compartments. We found that, under the selection regime,
migration rates are significantly overestimated with a stochastic mixture
model and a structured coalescent model in the Bayesian inference framework
BEAST2. Our results reveal that commonly used phylogeographic methods, which
assume neutral evolution, can significantly bias migration rate estimates in
selective regimes. This study underscores the need for assessing the
robustness of phylodynamic analysis with respect to more realistic selection
regimes.

## Data

The raw data used in the manuscript constitutes to about 600 GB of uncompressed
log files from the BEAST2 analysis and simulated sequences.
Additionally, there are several already processed datasets that are stored as
`csv` and can be loaded with common data analysis libraries or tools.

## Overview

The archive contains:

- `archive_250731.tar.gz`: Raw data
- `out/cache/<selector>.csv`: Processed data
- `README.md`: Description

## Usage

Use in conjunction with the code at [10.5281/zenodo.16744272](https://doi.org/10.5281/zenodo.16744272).