Benefits and limits of phasing alleles for network inference of allopolyploid complexes

Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared to haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pip..., , Included is a single pdf of the supplementary material as well as a tarball with all of the data used in the manuscript.
Download the tarball and within is a readme detailing contents including:
1) Control files and simulated sequence data for the single allotetraploid with BPP
2) A static release of the PATÉ pipeline used for phasing Dryopteris sequences in the manuscript
3) Dryopteris data used for analyses
4) BPP Control files, Julia scripts, and notes for repeating some of the empirical analyses, # Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

[https://doi.org/10.5061/dryad.5qfttdz53](https://doi.org/10.5061/dryad.5qfttdz53)

Contents include the simulated sequence data as well as the empirical *Dryopteris* data and some of the files used for analyses. Most of the code used throughout the manuscript is cited and available on github. However, we include a static version of [PATÉ](https://github.com/gtiley/Phasing) used at the time of writing and the control file options used for our analyses.

## Description of the data and file structure

### simulation

t1 - simulations for tau_h = 0.001 and theta = tau_h
t2 - simulations for tau_h = 0.001 and theta = 2 * tau_h
t3 - simulations for tau_h = 0.001 and theta = 3 * tau_h
t4 - simulations for tau_h = 0.001 and theta = 4 * tau_h
t5 - simulations for tau_h = 0.01 and theta = tau_h
t6 - simulations for tau_h = 0.01 and theta = 2 * tau_h
t7 - simulations for tau_h = 0.01 and theta = 3 * tau_h
t...