Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant-calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate to what extent the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele fil..., Data and supplementary material here are associated with the manuscript \"Reference genome choice and filtering thresholds jointly influence phylogenetic analyses\". Scripts can be found at https://github.com/jessicarick/refbias_scripts, and are archived on Zenodo at https://doi.org/10.5281/zenodo.5940690., , # Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

In addition to the supplemental methods, tables, and figures (**SUPPLEMENT\_Reference\_Bias\_in\_SNP\_based\_Phylogenetics\_SysBio.PDF**), there are four compressed directories included in this repository:

1. **simulation\_vcfs.tar.gz**: contains unfiltered VCFs for each of the simulation iterations, aligned to each of the reference genomes; each of these is named with the simulation date, tree height, simulation number, and reference genome identity (INT/EXT)
2. **empirical\_vcfs.tar.gz**: contains unfiltered VCFs for each of the empirical datasets (10 replicates for each clade), aligned to each of the reference genomes; each of these is named with the simulation number, and reference genome identity (INT/EXT)
3. **sim\_results\_raxml\_astral.tar.gz**: contains results for each combination of simulation, reference genome, and filtering scheme
* \"all-subsamp-raxml.trees\" contains inferred RA...