DOI: 10.5061/dryad.5qfttdz53
title: Benefits and limits of phasing alleles for network inference of allopolyploid complexes

description: 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 pipeline is
 especially appropriate for target enrichment data, where depth of coverage
 is typically high enough to phase entire loci. We provide an empirical
 example in the North American Dryopteris fern complex that demonstrates
 insights from phased data as well as the challenges of network inference.
 We establish that our pipeline (PATÉ: Phased Alleles from Target
 Enrichment data) is capable of recovering a high proportion of phased loci
 from both diploids and polyploids. These data may improve network
 estimates compared to using haplotype consensus assemblies by accurately
 inferring the direction of gene flow, but statistical non-identifiability
 of phylogenetic networks poses a barrier to inferring the evolutionary
 history of reticulate complexes.
description: 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 <em>Dryopteris </em>sequences in the
 manuscript 3) <em>Dryopteris </em>data used
 for analyses 4) BPP Control files, Julia scripts, and
 notes for repeating some of the empirical analyses
description: # 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 t8 - simulations for tau_h = 0.01 and theta = 4 * tau_h t9 - simulations for tau_h = 0.1 and theta = tau_h t10 - simulations for tau_h = 0.1 and theta = 2 * tau_h t11 - simulations for tau_h = 0.1 and theta = 3 * tau_h t12 - simulations for tau_h = 0.1 and theta = 4 * tau_h consensus.pl - script for creating random haplotype consesnus data from simulated sequences mkphy.pl - reformat simulated sequences to phylip format for gene tree estimation pickone.pl - randomly select only one similated sequence per species pn.consensus.jl.template - julia script used for SNaQ with consensus data pn.phase.jl.template - julia script used for phased data pn.pickone.jl.template - julia script used for pick one data pn.true.jl.template - julia script used for known gene trees pn.unphase.jl.template - julia script used for sequences with IUPAC codes pnDriver.pl - creates the julia scripts for various simulated data sets unphase.pl - collapses the simulated sequences per species into a single sequence with IUPAC codes ### PATE * phasedData - A copy of PATE at the time of writing. See more information at [https://github.com/gtiley/Phasing](https://github.com/gtiley/Phasing) * PATE.pl - the main PATE script * PATE.ctl - the PATE control file * ploidy.txt - the ploidy file * template.sh - the template submission script * helperScripts - helper functions * summaryStatsOutput-ALL - summary statistics for individuals * referenceSequences * .fasta - the supercontig fasta output for all indidivuals by locus ### Dryopteris\_analyses all_taxa * consensus - alignments, gene trees, species trees, and networks for consensus data * genotype - alignments, gene trees, species trees, and networks for gentyped data * phased - alignments, gene trees, species trees, and networks for phased data * pickone - alignments, gene trees, species trees, and networks for pickone data five_taxa - similar structure to above with alignments, gene trees, and networsk, but an extra directory level for the three focal allopolyploid tests * consensus * CGC - D. clintoniana is focal allopolyploid * IEC - D. campyloptera is focal allopolyploid * LGC - D. celsa is focal allopolyploid * genotype * phased * pickone three_taxa * consensus * Alignments - alignment files * CGC.bppDat - alignments reformatted into BPP's phylip format * CGC.spMap - the indidivual to species map for BPP * Converge - Indepdendent runs for models from BPP used to check convergence and estimate parameters prior to Bayes factor analyses. * 1 - model 1 * 2 - model 2 * 3 - model 3 * 4 - model 4 * 5 - model 5 * 6 - model 6 * genctl.pl - generate the control files for all models * runBPP.pl - create submission scripts and run BPP * genotyoe * phased * pickone ## Sharing/Access information Raw reads for empirical analyses are associate with NCBI BioProject PRJNA725004. Please consult the manuscript for details. ## Code/Software Additional manuscript resources can be found at: * [https://github.com/gtiley/Phasing](https://github.com/gtiley/Phasing) * [https://github.com/gtiley/bootSNaQ-MA](https://github.com/gtiley/bootSNaQ-MA) * [https://github.com/gtiley/bpp\\_simulationTools](https://github.com/gtiley/bpp_simulationTools)